Starting phenix.real_space_refine on Wed Mar 4 05:32:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6of3_20041/03_2026/6of3_20041.cif Found real_map, /net/cci-nas-00/data/ceres_data/6of3_20041/03_2026/6of3_20041.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6of3_20041/03_2026/6of3_20041.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6of3_20041/03_2026/6of3_20041.map" model { file = "/net/cci-nas-00/data/ceres_data/6of3_20041/03_2026/6of3_20041.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6of3_20041/03_2026/6of3_20041.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.657 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 7070 2.51 5 N 1938 2.21 5 O 2024 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11096 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1471 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 178} Chain breaks: 2 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 4045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4045 Classifications: {'peptide': 528} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 52, 'TRANS': 475} Unresolved chain links: 1 Chain breaks: 4 Unresolved chain link angles: 5 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1} 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: D, E Time building chain proxies: 3.23, per 1000 atoms: 0.29 Number of scatterers: 11096 At special positions: 0 Unit cell: (150.12, 87.48, 88.56, 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 2024 8.00 N 1938 7.00 C 7070 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: 0.85 Conformation dependent library (CDL) restraints added in 591.5 milliseconds 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2668 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 10 sheets defined 40.3% alpha, 18.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 11 through 23 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 removed outlier: 3.612A pdb=" N ARG A 97 " --> pdb=" O GLY A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 132 Processing helix chain 'A' and resid 134 through 146 removed outlier: 3.835A 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: 3.887A pdb=" N GLY A 175 " --> pdb=" O LYS A 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 202 removed outlier: 3.505A pdb=" N LEU B 200 " --> pdb=" O THR B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 211 removed outlier: 3.608A 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 258 removed outlier: 3.704A pdb=" N ARG B 258 " --> pdb=" O THR B 254 " (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 removed outlier: 3.758A pdb=" N ASP B 407 " --> pdb=" O GLY B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 443 removed outlier: 3.621A pdb=" N SER B 443 " --> pdb=" O ALA B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 484 removed outlier: 3.529A pdb=" N PHE B 483 " --> pdb=" O MET B 479 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N HIS B 484 " --> pdb=" O GLN B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 544 removed outlier: 4.226A pdb=" N SER B 540 " --> pdb=" O PRO B 536 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ASP B 541 " --> pdb=" O GLU B 537 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN B 544 " --> pdb=" O SER B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 625 No H-bonds generated for 'chain 'B' and resid 623 through 625' Processing helix chain 'B' and resid 654 through 660 Processing helix chain 'B' and resid 676 through 691 removed outlier: 4.188A pdb=" N TYR B 680 " --> pdb=" O PRO B 676 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL B 681 " --> pdb=" O THR B 677 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLY B 683 " --> pdb=" O ALA B 679 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N LEU B 684 " --> pdb=" O TYR B 680 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 23 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 removed outlier: 3.613A pdb=" N ARG D 97 " --> pdb=" O GLY D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 132 Processing helix chain 'D' and resid 134 through 146 removed outlier: 3.835A 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: 3.887A pdb=" N GLY D 175 " --> pdb=" O LYS D 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 202 removed outlier: 3.504A pdb=" N LEU E 200 " --> pdb=" O THR E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 211 removed outlier: 3.609A 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 258 removed outlier: 3.704A pdb=" N ARG E 258 " --> pdb=" O THR E 254 " (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 removed outlier: 3.759A pdb=" N ASP E 407 " --> pdb=" O GLY E 403 " (cutoff:3.500A) Processing helix chain 'E' and resid 429 through 443 removed outlier: 3.620A pdb=" N SER E 443 " --> pdb=" O ALA E 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 470 through 484 removed outlier: 3.529A pdb=" N PHE E 483 " --> pdb=" O MET E 479 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N HIS E 484 " --> pdb=" O GLN E 480 " (cutoff:3.500A) Processing helix chain 'E' and resid 535 through 544 removed outlier: 4.227A pdb=" N SER E 540 " --> pdb=" O PRO E 536 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ASP E 541 " --> pdb=" O GLU E 537 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN E 544 " --> pdb=" O SER E 540 " (cutoff:3.500A) Processing helix chain 'E' and resid 623 through 625 No H-bonds generated for 'chain 'E' and resid 623 through 625' Processing helix chain 'E' and resid 654 through 660 Processing helix chain 'E' and resid 676 through 691 removed outlier: 4.189A pdb=" N TYR E 680 " --> pdb=" O PRO E 676 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N VAL E 681 " --> pdb=" O THR E 677 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLY E 683 " --> pdb=" O ALA E 679 " (cutoff:3.500A) removed outlier: 4.501A 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: 7.347A pdb=" N GLU B 646 " --> pdb=" O VAL B 638 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N VAL B 638 " --> pdb=" O GLU B 646 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N HIS B 648 " --> pdb=" O ARG B 636 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N LEU B 550 " --> pdb=" O VAL B 630 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LEU B 632 " --> pdb=" O MET B 548 " (cutoff:3.500A) removed outlier: 6.577A 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: 3.920A pdb=" N GLU B 153 " --> pdb=" O ALA B 184 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ASP B 186 " --> pdb=" O GLN B 151 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N GLN B 151 " --> pdb=" O ASP B 186 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N VAL B 188 " --> pdb=" O VAL B 149 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N VAL B 149 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N GLU B 190 " --> pdb=" O VAL B 147 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N VAL B 147 " --> pdb=" O GLU B 190 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU B 192 " --> pdb=" O TYR B 145 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N TYR B 145 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY B 143 " --> pdb=" O ALA B 172 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 159 through 161 removed outlier: 3.572A pdb=" N LEU B 142 " --> pdb=" O GLN B 222 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 351 through 358 removed outlier: 7.010A pdb=" N LEU B 320 " --> pdb=" O VAL B 354 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N MET B 356 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL B 318 " --> pdb=" O MET B 356 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N MET B 301 " --> pdb=" O VAL B 394 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N ASN B 396 " --> pdb=" O MET B 301 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N LEU B 303 " --> pdb=" O ASN B 396 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 4 through 6 Processing sheet with id=AA7, first strand: chain 'D' and resid 347 through 349 removed outlier: 7.347A pdb=" N GLU E 646 " --> pdb=" O VAL E 638 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N VAL E 638 " --> pdb=" O GLU E 646 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N HIS E 648 " --> pdb=" O ARG E 636 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N LEU E 550 " --> pdb=" O VAL E 630 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LEU E 632 " --> pdb=" O MET E 548 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N MET E 548 " --> pdb=" O LEU E 632 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 122 through 125 removed outlier: 3.920A pdb=" N GLU E 153 " --> pdb=" O ALA E 184 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ASP E 186 " --> pdb=" O GLN E 151 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N GLN E 151 " --> pdb=" O ASP E 186 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N VAL E 188 " --> pdb=" O VAL E 149 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N VAL E 149 " --> pdb=" O VAL E 188 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N GLU E 190 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N VAL E 147 " --> pdb=" O GLU E 190 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU E 192 " --> pdb=" O TYR E 145 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N TYR E 145 " --> pdb=" O LEU E 192 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY E 143 " --> pdb=" O ALA E 172 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 159 through 161 removed outlier: 3.573A pdb=" N LEU E 142 " --> pdb=" O GLN E 222 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 351 through 358 removed outlier: 7.010A pdb=" N LEU E 320 " --> pdb=" O VAL E 354 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N MET E 356 " --> pdb=" O VAL E 318 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL E 318 " --> pdb=" O MET E 356 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N MET E 301 " --> pdb=" O VAL E 394 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N ASN E 396 " --> pdb=" O MET E 301 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N LEU E 303 " --> pdb=" O ASN E 396 " (cutoff:3.500A) 490 hydrogen bonds defined for protein. 1398 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.90 Time building geometry restraints manager: 1.20 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: 3761 1.37 - 1.51: 3752 1.51 - 1.65: 3795 1.65 - 1.80: 60 1.80 - 1.94: 30 Bond restraints: 11398 Sorted by residual: bond pdb=" C GLN E 115 " pdb=" N PRO E 116 " ideal model delta sigma weight residual 1.334 1.401 -0.067 2.34e-02 1.83e+03 8.14e+00 bond pdb=" C GLN B 115 " pdb=" N PRO B 116 " ideal model delta sigma weight residual 1.334 1.400 -0.066 2.34e-02 1.83e+03 8.06e+00 bond pdb=" O3G AGS E 801 " pdb=" PG AGS E 801 " ideal model delta sigma weight residual 1.558 1.503 0.055 2.00e-02 2.50e+03 7.55e+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 7.37e+00 bond pdb=" O2G AGS B 801 " pdb=" PG AGS B 801 " ideal model delta sigma weight residual 1.557 1.503 0.054 2.00e-02 2.50e+03 7.31e+00 ... (remaining 11393 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.30: 14802 3.30 - 6.61: 652 6.61 - 9.91: 86 9.91 - 13.21: 24 13.21 - 16.52: 6 Bond angle restraints: 15570 Sorted by residual: angle pdb=" C THR B 641 " pdb=" N ALA B 642 " pdb=" CA ALA B 642 " ideal model delta sigma weight residual 121.54 138.06 -16.52 1.91e+00 2.74e-01 7.48e+01 angle pdb=" C THR E 641 " pdb=" N ALA E 642 " pdb=" CA ALA E 642 " ideal model delta sigma weight residual 121.54 138.00 -16.46 1.91e+00 2.74e-01 7.42e+01 angle pdb=" C ALA E 184 " pdb=" N ASN E 185 " pdb=" CA ASN E 185 " ideal model delta sigma weight residual 121.54 137.98 -16.44 1.91e+00 2.74e-01 7.41e+01 angle pdb=" C ALA B 184 " pdb=" N ASN B 185 " pdb=" CA ASN B 185 " ideal model delta sigma weight residual 121.54 137.97 -16.43 1.91e+00 2.74e-01 7.40e+01 angle pdb=" C LYS B 293 " pdb=" N SER B 294 " pdb=" CA SER B 294 " ideal model delta sigma weight residual 121.54 137.35 -15.81 1.91e+00 2.74e-01 6.86e+01 ... (remaining 15565 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.07: 6621 33.07 - 66.13: 181 66.13 - 99.20: 2 99.20 - 132.26: 0 132.26 - 165.33: 2 Dihedral angle restraints: 6806 sinusoidal: 2688 harmonic: 4118 Sorted by residual: dihedral pdb=" CA ALA E 184 " pdb=" C ALA E 184 " pdb=" N ASN E 185 " pdb=" CA ASN E 185 " ideal model delta harmonic sigma weight residual -180.00 -136.55 -43.45 0 5.00e+00 4.00e-02 7.55e+01 dihedral pdb=" CA ALA B 184 " pdb=" C ALA B 184 " pdb=" N ASN B 185 " pdb=" CA ASN B 185 " ideal model delta harmonic sigma weight residual -180.00 -136.58 -43.42 0 5.00e+00 4.00e-02 7.54e+01 dihedral pdb=" CA TYR E 225 " pdb=" C TYR E 225 " pdb=" N THR E 226 " pdb=" CA THR E 226 " ideal model delta harmonic sigma weight residual -180.00 -145.87 -34.13 0 5.00e+00 4.00e-02 4.66e+01 ... (remaining 6803 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1201 0.066 - 0.132: 370 0.132 - 0.198: 133 0.198 - 0.264: 35 0.264 - 0.330: 5 Chirality restraints: 1744 Sorted by residual: chirality pdb=" CB ILE B 391 " pdb=" CA ILE B 391 " pdb=" CG1 ILE B 391 " pdb=" CG2 ILE B 391 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" CB ILE E 391 " pdb=" CA ILE E 391 " pdb=" CG1 ILE E 391 " pdb=" CG2 ILE E 391 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" CB VAL B 667 " pdb=" CA VAL B 667 " pdb=" CG1 VAL B 667 " pdb=" CG2 VAL B 667 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.14e+00 ... (remaining 1741 not shown) Planarity restraints: 1990 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN E 644 " 0.018 2.00e-02 2.50e+03 3.46e-02 1.20e+01 pdb=" C ASN E 644 " -0.060 2.00e-02 2.50e+03 pdb=" O ASN E 644 " 0.022 2.00e-02 2.50e+03 pdb=" N PRO E 645 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 644 " -0.017 2.00e-02 2.50e+03 3.41e-02 1.16e+01 pdb=" C ASN B 644 " 0.059 2.00e-02 2.50e+03 pdb=" O ASN B 644 " -0.021 2.00e-02 2.50e+03 pdb=" N PRO B 645 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS E 259 " -0.053 5.00e-02 4.00e+02 7.98e-02 1.02e+01 pdb=" N PRO E 260 " 0.138 5.00e-02 4.00e+02 pdb=" CA PRO E 260 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO E 260 " -0.045 5.00e-02 4.00e+02 ... (remaining 1987 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 106 2.63 - 3.20: 9297 3.20 - 3.76: 15729 3.76 - 4.33: 19753 4.33 - 4.90: 34995 Nonbonded interactions: 79880 Sorted by model distance: nonbonded pdb=" O2B AGS B 801 " pdb="MG MG B 802 " model vdw 2.058 2.170 nonbonded pdb=" O2B AGS E 801 " pdb="MG MG E 802 " model vdw 2.059 2.170 nonbonded pdb=" O3G AGS E 801 " pdb="MG MG E 802 " model vdw 2.131 2.170 nonbonded pdb=" O3G AGS B 801 " pdb="MG MG B 802 " model vdw 2.131 2.170 nonbonded pdb=" OG SER B 275 " pdb="MG MG B 802 " model vdw 2.188 2.170 ... (remaining 79875 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } 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: 1.130 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: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.890 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6305 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 : 0.008 0.069 11398 Z= 0.376 Angle : 1.590 16.517 15570 Z= 0.886 Chirality : 0.076 0.330 1744 Planarity : 0.011 0.080 1990 Dihedral : 14.843 165.331 4138 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 2.01 % Allowed : 16.07 % Favored : 81.92 % Rotamer: Outliers : 0.85 % Allowed : 4.67 % Favored : 94.48 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.36 (0.18), residues: 1394 helix: -2.16 (0.17), residues: 446 sheet: -1.48 (0.32), residues: 234 loop : -4.03 (0.19), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 355 TYR 0.036 0.004 TYR E 685 PHE 0.029 0.004 PHE D 104 TRP 0.040 0.003 TRP B 297 HIS 0.007 0.002 HIS B 334 Details of bonding type rmsd covalent geometry : bond 0.00810 (11398) covalent geometry : angle 1.59035 (15570) hydrogen bonds : bond 0.19908 ( 490) hydrogen bonds : angle 6.07747 ( 1398) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 366 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 ILE cc_start: 0.7568 (mm) cc_final: 0.7277 (mm) REVERT: A 23 TYR cc_start: 0.7407 (m-80) cc_final: 0.7144 (m-80) REVERT: B 364 PRO cc_start: 0.5826 (Cg_exo) cc_final: 0.5619 (Cg_endo) REVERT: D 5 ILE cc_start: 0.7433 (mm) cc_final: 0.7119 (mm) REVERT: E 222 GLN cc_start: 0.7540 (OUTLIER) cc_final: 0.7207 (pp30) REVERT: E 349 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7355 (mp0) REVERT: E 432 THR cc_start: 0.8161 (t) cc_final: 0.7928 (m) outliers start: 10 outliers final: 4 residues processed: 372 average time/residue: 0.4495 time to fit residues: 183.1441 Evaluate side-chains 227 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 222 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain E residue 222 GLN Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 668 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 0.1980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN B 144 ASN B 171 HIS B 198 GLN ** B 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 ASN B 689 ASN D 143 GLN E 117 ASN E 144 ASN E 174 HIS E 185 ASN E 222 GLN ** E 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 644 ASN E 689 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.115608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.094800 restraints weight = 18465.824| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 3.34 r_work: 0.3184 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.3798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 11398 Z= 0.192 Angle : 0.960 12.750 15570 Z= 0.469 Chirality : 0.049 0.181 1744 Planarity : 0.007 0.055 1990 Dihedral : 10.071 161.634 1588 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.86 % Allowed : 8.75 % Favored : 90.39 % Rotamer: Outliers : 5.77 % Allowed : 16.55 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.23), residues: 1394 helix: 2.18 (0.23), residues: 450 sheet: -0.85 (0.35), residues: 206 loop : -2.80 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 662 TYR 0.021 0.003 TYR E 685 PHE 0.044 0.003 PHE E 139 TRP 0.023 0.002 TRP B 722 HIS 0.014 0.002 HIS B 150 Details of bonding type rmsd covalent geometry : bond 0.00424 (11398) covalent geometry : angle 0.96014 (15570) hydrogen bonds : bond 0.05732 ( 490) hydrogen bonds : angle 5.00209 ( 1398) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 249 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 141 ILE cc_start: 0.8567 (mt) cc_final: 0.8335 (mp) REVERT: B 283 ASN cc_start: 0.6333 (m-40) cc_final: 0.4632 (t0) REVERT: B 318 VAL cc_start: 0.7381 (m) cc_final: 0.7081 (m) REVERT: B 364 PRO cc_start: 0.5837 (Cg_exo) cc_final: 0.5619 (Cg_endo) REVERT: B 479 MET cc_start: 0.7682 (tpp) cc_final: 0.6861 (tpt) REVERT: D 94 TYR cc_start: 0.5243 (OUTLIER) cc_final: 0.5036 (m-80) REVERT: D 172 LYS cc_start: 0.7369 (OUTLIER) cc_final: 0.6902 (ttmt) REVERT: E 367 ASP cc_start: 0.6602 (t0) cc_final: 0.6213 (m-30) REVERT: E 479 MET cc_start: 0.7667 (tpp) cc_final: 0.7441 (tpt) REVERT: E 537 GLU cc_start: 0.8033 (mp0) cc_final: 0.7761 (mp0) REVERT: E 546 MET cc_start: 0.7497 (mmm) cc_final: 0.7251 (mpp) REVERT: E 644 ASN cc_start: 0.6531 (OUTLIER) cc_final: 0.6238 (m-40) outliers start: 68 outliers final: 21 residues processed: 288 average time/residue: 0.4106 time to fit residues: 131.4135 Evaluate side-chains 229 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 205 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 174 HIS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain D residue 172 LYS Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 249 ILE Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 353 THR Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 623 SER Chi-restraints excluded: chain E residue 639 SER Chi-restraints excluded: chain E residue 644 ASN Chi-restraints excluded: chain E residue 668 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 0.8980 chunk 118 optimal weight: 0.9980 chunk 3 optimal weight: 6.9990 chunk 100 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 54 optimal weight: 0.0770 chunk 98 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 171 HIS B 357 HIS B 644 ASN B 689 ASN D 21 GLN D 26 HIS E 532 HIS E 644 ASN E 689 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.116987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.096100 restraints weight = 18650.046| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 3.36 r_work: 0.3208 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.5271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 11398 Z= 0.179 Angle : 0.864 12.137 15570 Z= 0.420 Chirality : 0.046 0.181 1744 Planarity : 0.006 0.055 1990 Dihedral : 9.276 157.465 1583 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.75 % Favored : 90.82 % Rotamer: Outliers : 6.11 % Allowed : 18.34 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.23), residues: 1394 helix: 2.39 (0.23), residues: 486 sheet: -0.90 (0.33), residues: 210 loop : -2.51 (0.22), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 205 TYR 0.020 0.002 TYR E 225 PHE 0.032 0.003 PHE A 107 TRP 0.017 0.002 TRP E 500 HIS 0.008 0.001 HIS E 532 Details of bonding type rmsd covalent geometry : bond 0.00409 (11398) covalent geometry : angle 0.86377 (15570) hydrogen bonds : bond 0.05002 ( 490) hydrogen bonds : angle 4.53837 ( 1398) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 238 time to evaluate : 0.292 Fit side-chains REVERT: A 21 GLN cc_start: 0.7473 (OUTLIER) cc_final: 0.7176 (tt0) REVERT: B 141 ILE cc_start: 0.8918 (mt) cc_final: 0.8630 (mp) REVERT: B 477 MET cc_start: 0.8280 (mtp) cc_final: 0.8035 (mpp) REVERT: B 479 MET cc_start: 0.8386 (tpp) cc_final: 0.7458 (tpt) REVERT: B 567 ASP cc_start: 0.5991 (OUTLIER) cc_final: 0.5388 (t0) REVERT: B 672 LYS cc_start: 0.8544 (mmmm) cc_final: 0.8208 (mmmt) REVERT: D 5 ILE cc_start: 0.8912 (mm) cc_final: 0.8696 (pp) REVERT: D 21 GLN cc_start: 0.7253 (OUTLIER) cc_final: 0.6961 (tt0) REVERT: D 68 HIS cc_start: 0.8633 (t70) cc_final: 0.8413 (t-170) REVERT: E 147 VAL cc_start: 0.8572 (OUTLIER) cc_final: 0.8372 (t) REVERT: E 499 GLU cc_start: 0.7577 (pm20) cc_final: 0.7368 (pm20) REVERT: E 525 LEU cc_start: 0.6953 (OUTLIER) cc_final: 0.6570 (tp) REVERT: E 537 GLU cc_start: 0.8294 (mp0) cc_final: 0.7991 (mp0) REVERT: E 567 ASP cc_start: 0.5936 (OUTLIER) cc_final: 0.5537 (OUTLIER) REVERT: E 672 LYS cc_start: 0.8785 (mmmm) cc_final: 0.8540 (mmmt) outliers start: 72 outliers final: 27 residues processed: 288 average time/residue: 0.3858 time to fit residues: 123.4598 Evaluate side-chains 239 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 207 time to evaluate : 0.384 ------------------------------------------------------------------------------- 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 156 ILE Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 174 HIS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 567 ASP Chi-restraints excluded: chain B residue 623 SER Chi-restraints excluded: chain B residue 650 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 147 VAL Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 249 ILE Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 353 THR Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 474 LEU Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain E residue 525 LEU Chi-restraints excluded: chain E residue 567 ASP Chi-restraints excluded: chain E residue 623 SER Chi-restraints excluded: chain E residue 639 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 82 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 133 optimal weight: 0.9980 chunk 120 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN B 283 ASN ** B 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 26 HIS E 144 ASN E 174 HIS ** E 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 ASN ** E 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 689 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.118865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.098023 restraints weight = 18902.449| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 3.45 r_work: 0.3187 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.7693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 11398 Z= 0.212 Angle : 0.868 14.921 15570 Z= 0.426 Chirality : 0.048 0.199 1744 Planarity : 0.007 0.053 1990 Dihedral : 9.077 152.048 1579 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.82 % Favored : 91.03 % Rotamer: Outliers : 6.79 % Allowed : 21.22 % Favored : 71.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.23), residues: 1394 helix: 2.35 (0.23), residues: 486 sheet: -0.96 (0.35), residues: 200 loop : -2.41 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 123 TYR 0.019 0.002 TYR E 685 PHE 0.042 0.003 PHE A 107 TRP 0.026 0.002 TRP E 500 HIS 0.014 0.002 HIS E 174 Details of bonding type rmsd covalent geometry : bond 0.00492 (11398) covalent geometry : angle 0.86797 (15570) hydrogen bonds : bond 0.05443 ( 490) hydrogen bonds : angle 4.45535 ( 1398) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 258 time to evaluate : 0.290 Fit side-chains REVERT: A 94 TYR cc_start: 0.7764 (OUTLIER) cc_final: 0.7488 (m-80) REVERT: B 141 ILE cc_start: 0.9155 (mt) cc_final: 0.8903 (mp) REVERT: B 281 LEU cc_start: 0.8608 (tt) cc_final: 0.8402 (tp) REVERT: B 309 GLN cc_start: 0.8229 (tt0) cc_final: 0.8014 (mt0) REVERT: B 366 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8361 (mm) REVERT: B 367 ASP cc_start: 0.7737 (t0) cc_final: 0.7290 (m-30) REVERT: B 525 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8130 (tp) REVERT: B 567 ASP cc_start: 0.6266 (OUTLIER) cc_final: 0.5841 (t0) REVERT: B 664 ASP cc_start: 0.4664 (t0) cc_final: 0.4455 (m-30) REVERT: B 672 LYS cc_start: 0.8694 (mmmm) cc_final: 0.8437 (mmmt) REVERT: D 21 GLN cc_start: 0.8023 (OUTLIER) cc_final: 0.7765 (tt0) REVERT: D 23 TYR cc_start: 0.8134 (m-80) cc_final: 0.7684 (m-80) REVERT: D 72 SER cc_start: 0.8625 (t) cc_final: 0.8322 (p) REVERT: D 153 THR cc_start: 0.8466 (m) cc_final: 0.8159 (p) REVERT: D 172 LYS cc_start: 0.8362 (tppt) cc_final: 0.7936 (ttmt) REVERT: E 237 ARG cc_start: 0.7721 (ptp-170) cc_final: 0.7388 (mtm-85) REVERT: E 281 LEU cc_start: 0.8709 (tt) cc_final: 0.8503 (tp) REVERT: E 333 CYS cc_start: 0.8192 (t) cc_final: 0.7894 (m) REVERT: E 477 MET cc_start: 0.8846 (OUTLIER) cc_final: 0.8496 (mtm) REVERT: E 525 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8158 (tp) REVERT: E 554 GLU cc_start: 0.8299 (tt0) cc_final: 0.7848 (mt-10) REVERT: E 618 THR cc_start: 0.9146 (m) cc_final: 0.8909 (t) REVERT: E 629 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8626 (tt) REVERT: E 662 ARG cc_start: 0.8512 (tpp80) cc_final: 0.7903 (ttt-90) REVERT: E 672 LYS cc_start: 0.8931 (mmmm) cc_final: 0.8657 (mmmt) outliers start: 80 outliers final: 35 residues processed: 312 average time/residue: 0.3905 time to fit residues: 135.4825 Evaluate side-chains 241 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 198 time to evaluate : 0.421 ------------------------------------------------------------------------------- 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 174 HIS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 567 ASP Chi-restraints excluded: chain B residue 623 SER Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 725 MET Chi-restraints excluded: chain D residue 21 GLN Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 249 ILE Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 353 THR Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 477 MET Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain E residue 525 LEU Chi-restraints excluded: chain E residue 567 ASP Chi-restraints excluded: chain E residue 623 SER Chi-restraints excluded: chain E residue 629 LEU Chi-restraints excluded: chain E residue 639 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 126 optimal weight: 0.4980 chunk 18 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 136 optimal weight: 0.0050 chunk 129 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 113 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN B 144 ASN B 171 HIS ** B 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 ASN B 648 HIS D 26 HIS E 174 HIS ** E 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 689 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.117599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.095651 restraints weight = 18469.205| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 3.44 r_work: 0.3192 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.8157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 11398 Z= 0.146 Angle : 0.772 15.831 15570 Z= 0.369 Chirality : 0.044 0.158 1744 Planarity : 0.006 0.049 1990 Dihedral : 8.831 151.023 1579 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.82 % Favored : 92.04 % Rotamer: Outliers : 5.69 % Allowed : 25.55 % Favored : 68.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.23), residues: 1394 helix: 2.71 (0.23), residues: 486 sheet: -0.91 (0.36), residues: 190 loop : -2.18 (0.21), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 289 TYR 0.012 0.001 TYR B 382 PHE 0.034 0.002 PHE D 107 TRP 0.015 0.001 TRP A 347 HIS 0.008 0.001 HIS E 174 Details of bonding type rmsd covalent geometry : bond 0.00322 (11398) covalent geometry : angle 0.77175 (15570) hydrogen bonds : bond 0.04473 ( 490) hydrogen bonds : angle 4.27155 ( 1398) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 216 time to evaluate : 0.490 Fit side-chains revert: symmetry clash REVERT: A 94 TYR cc_start: 0.7727 (OUTLIER) cc_final: 0.7415 (m-80) REVERT: B 141 ILE cc_start: 0.9089 (mt) cc_final: 0.8848 (mp) REVERT: B 155 THR cc_start: 0.8192 (m) cc_final: 0.7672 (p) REVERT: B 166 ASP cc_start: 0.8056 (t0) cc_final: 0.7819 (t0) REVERT: B 237 ARG cc_start: 0.7750 (mtt180) cc_final: 0.7478 (mtm-85) REVERT: B 281 LEU cc_start: 0.8645 (tt) cc_final: 0.8433 (tp) REVERT: B 309 GLN cc_start: 0.8320 (tt0) cc_final: 0.8086 (mt0) REVERT: B 367 ASP cc_start: 0.7736 (OUTLIER) cc_final: 0.7366 (m-30) REVERT: B 407 ASP cc_start: 0.8851 (t0) cc_final: 0.8585 (m-30) REVERT: B 525 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8163 (tp) REVERT: B 662 ARG cc_start: 0.8392 (tpp80) cc_final: 0.7767 (ttt-90) REVERT: D 23 TYR cc_start: 0.8195 (m-80) cc_final: 0.7840 (m-80) REVERT: D 25 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.7290 (pm20) REVERT: D 72 SER cc_start: 0.8494 (t) cc_final: 0.8248 (p) REVERT: D 153 THR cc_start: 0.8396 (m) cc_final: 0.8124 (p) REVERT: D 172 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.7867 (ttmt) REVERT: E 237 ARG cc_start: 0.7747 (OUTLIER) cc_final: 0.7417 (mtm-85) REVERT: E 281 LEU cc_start: 0.8728 (tt) cc_final: 0.8520 (tp) REVERT: E 333 CYS cc_start: 0.8174 (t) cc_final: 0.7743 (m) REVERT: E 407 ASP cc_start: 0.8799 (t0) cc_final: 0.8534 (m-30) REVERT: E 525 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8210 (tp) REVERT: E 554 GLU cc_start: 0.8187 (tt0) cc_final: 0.7615 (mt-10) REVERT: E 618 THR cc_start: 0.9143 (m) cc_final: 0.8925 (t) REVERT: E 662 ARG cc_start: 0.8528 (tpp80) cc_final: 0.8019 (ttt-90) outliers start: 67 outliers final: 30 residues processed: 261 average time/residue: 0.3709 time to fit residues: 108.1005 Evaluate side-chains 230 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 193 time to evaluate : 0.393 ------------------------------------------------------------------------------- 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 156 ILE Chi-restraints excluded: chain B residue 174 HIS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 623 SER Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 720 VAL Chi-restraints excluded: chain D residue 25 GLU Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 172 LYS Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 237 ARG Chi-restraints excluded: chain E residue 249 ILE Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain E residue 525 LEU Chi-restraints excluded: chain E residue 543 ILE Chi-restraints excluded: chain E residue 623 SER Chi-restraints excluded: chain E residue 720 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 100 optimal weight: 8.9990 chunk 110 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 138 optimal weight: 0.4980 chunk 90 optimal weight: 0.3980 chunk 54 optimal weight: 3.9990 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 21 GLN B 357 HIS ** B 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 21 GLN D 26 HIS E 110 HIS ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 151 GLN E 171 HIS E 480 GLN ** E 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.115135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.092835 restraints weight = 18613.224| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 3.47 r_work: 0.3117 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.9247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11398 Z= 0.209 Angle : 0.811 15.077 15570 Z= 0.392 Chirality : 0.047 0.216 1744 Planarity : 0.006 0.050 1990 Dihedral : 8.609 147.443 1579 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.97 % Favored : 90.89 % Rotamer: Outliers : 6.54 % Allowed : 23.68 % Favored : 69.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.23), residues: 1394 helix: 2.49 (0.23), residues: 498 sheet: -0.66 (0.35), residues: 198 loop : -2.22 (0.22), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 522 TYR 0.016 0.002 TYR E 382 PHE 0.041 0.003 PHE D 107 TRP 0.024 0.002 TRP E 400 HIS 0.007 0.001 HIS B 150 Details of bonding type rmsd covalent geometry : bond 0.00487 (11398) covalent geometry : angle 0.81079 (15570) hydrogen bonds : bond 0.05576 ( 490) hydrogen bonds : angle 4.35484 ( 1398) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 226 time to evaluate : 0.378 Fit side-chains REVERT: A 94 TYR cc_start: 0.8125 (OUTLIER) cc_final: 0.7752 (m-80) REVERT: A 165 TRP cc_start: 0.8601 (t60) cc_final: 0.8350 (t60) REVERT: B 141 ILE cc_start: 0.9170 (mt) cc_final: 0.8892 (mp) REVERT: B 155 THR cc_start: 0.8323 (m) cc_final: 0.7976 (p) REVERT: B 237 ARG cc_start: 0.8090 (mtt180) cc_final: 0.7831 (mtm-85) REVERT: B 367 ASP cc_start: 0.8016 (OUTLIER) cc_final: 0.7713 (m-30) REVERT: B 407 ASP cc_start: 0.8893 (t0) cc_final: 0.8648 (m-30) REVERT: B 499 GLU cc_start: 0.8021 (pm20) cc_final: 0.7616 (tt0) REVERT: B 525 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8361 (tp) REVERT: B 646 GLU cc_start: 0.8083 (pt0) cc_final: 0.7792 (pp20) REVERT: B 662 ARG cc_start: 0.8474 (tpp80) cc_final: 0.8008 (ttt-90) REVERT: D 23 TYR cc_start: 0.8467 (m-80) cc_final: 0.7797 (m-80) REVERT: D 25 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7403 (pm20) REVERT: D 153 THR cc_start: 0.8471 (m) cc_final: 0.8223 (p) REVERT: D 172 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8390 (ttmt) REVERT: E 222 GLN cc_start: 0.8288 (pt0) cc_final: 0.7889 (pp30) REVERT: E 333 CYS cc_start: 0.8453 (OUTLIER) cc_final: 0.8219 (m) REVERT: E 382 TYR cc_start: 0.8263 (t80) cc_final: 0.7904 (t80) REVERT: E 391 ILE cc_start: 0.8744 (pt) cc_final: 0.8541 (pt) REVERT: E 407 ASP cc_start: 0.8827 (t0) cc_final: 0.8603 (m-30) REVERT: E 477 MET cc_start: 0.9023 (OUTLIER) cc_final: 0.8772 (mtm) REVERT: E 525 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8407 (tp) REVERT: E 554 GLU cc_start: 0.8594 (tt0) cc_final: 0.8053 (mt-10) REVERT: E 625 GLN cc_start: 0.7871 (OUTLIER) cc_final: 0.7564 (tt0) REVERT: E 662 ARG cc_start: 0.8598 (tpp80) cc_final: 0.7964 (ttp80) REVERT: E 664 ASP cc_start: 0.5522 (OUTLIER) cc_final: 0.5034 (m-30) outliers start: 77 outliers final: 45 residues processed: 281 average time/residue: 0.3824 time to fit residues: 119.3530 Evaluate side-chains 253 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 198 time to evaluate : 0.429 ------------------------------------------------------------------------------- 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 156 ILE Chi-restraints excluded: chain B residue 174 HIS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 623 SER Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain D residue 25 GLU Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 172 LYS Chi-restraints excluded: chain E residue 109 MET Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 333 CYS Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 338 SER Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 425 SER Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 477 MET Chi-restraints excluded: chain E residue 505 LEU Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain E residue 525 LEU Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain E residue 543 ILE Chi-restraints excluded: chain E residue 623 SER Chi-restraints excluded: chain E residue 625 GLN Chi-restraints excluded: chain E residue 664 ASP Chi-restraints excluded: chain E residue 720 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 107 optimal weight: 0.4980 chunk 99 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 5 optimal weight: 0.0170 overall best weight: 0.6818 ------------------------------------------------------------------------------- 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 ** B 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 21 GLN D 143 GLN ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 242 HIS ** E 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 689 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.117498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.095368 restraints weight = 18421.065| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 3.46 r_work: 0.3156 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.9567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11398 Z= 0.138 Angle : 0.760 15.282 15570 Z= 0.361 Chirality : 0.044 0.205 1744 Planarity : 0.006 0.050 1990 Dihedral : 8.506 146.618 1579 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.82 % Favored : 92.04 % Rotamer: Outliers : 5.35 % Allowed : 26.32 % Favored : 68.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.23), residues: 1394 helix: 2.69 (0.23), residues: 496 sheet: -0.86 (0.33), residues: 212 loop : -2.08 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 279 TYR 0.011 0.001 TYR E 382 PHE 0.027 0.002 PHE A 107 TRP 0.013 0.001 TRP B 400 HIS 0.006 0.001 HIS D 68 Details of bonding type rmsd covalent geometry : bond 0.00322 (11398) covalent geometry : angle 0.75966 (15570) hydrogen bonds : bond 0.04333 ( 490) hydrogen bonds : angle 4.16686 ( 1398) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 199 time to evaluate : 0.307 Fit side-chains REVERT: A 94 TYR cc_start: 0.8020 (OUTLIER) cc_final: 0.7660 (m-80) REVERT: A 362 ILE cc_start: 0.9268 (tt) cc_final: 0.8796 (pt) REVERT: B 141 ILE cc_start: 0.9163 (mt) cc_final: 0.8921 (mp) REVERT: B 155 THR cc_start: 0.8401 (m) cc_final: 0.8058 (p) REVERT: B 237 ARG cc_start: 0.8124 (mtt180) cc_final: 0.7750 (mtm-85) REVERT: B 309 GLN cc_start: 0.8457 (tt0) cc_final: 0.8178 (mt0) REVERT: B 367 ASP cc_start: 0.7894 (OUTLIER) cc_final: 0.7606 (OUTLIER) REVERT: B 525 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8382 (tp) REVERT: B 662 ARG cc_start: 0.8514 (tpp80) cc_final: 0.8044 (ttt-90) REVERT: D 25 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7494 (pm20) REVERT: D 107 PHE cc_start: 0.8045 (t80) cc_final: 0.7835 (t80) REVERT: D 172 LYS cc_start: 0.8654 (tppt) cc_final: 0.8295 (tmmt) REVERT: D 362 ILE cc_start: 0.9262 (tt) cc_final: 0.8801 (pt) REVERT: E 141 ILE cc_start: 0.8795 (mt) cc_final: 0.8529 (mp) REVERT: E 183 THR cc_start: 0.8167 (p) cc_final: 0.7941 (t) REVERT: E 222 GLN cc_start: 0.8229 (pt0) cc_final: 0.7643 (pp30) REVERT: E 237 ARG cc_start: 0.8000 (OUTLIER) cc_final: 0.7697 (mtm-85) REVERT: E 333 CYS cc_start: 0.8359 (OUTLIER) cc_final: 0.8093 (m) REVERT: E 477 MET cc_start: 0.9037 (OUTLIER) cc_final: 0.8744 (mtm) REVERT: E 525 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8484 (tp) REVERT: E 554 GLU cc_start: 0.8535 (tt0) cc_final: 0.8023 (mt-10) REVERT: E 662 ARG cc_start: 0.8632 (tpp80) cc_final: 0.7987 (ttp80) outliers start: 63 outliers final: 35 residues processed: 244 average time/residue: 0.3555 time to fit residues: 97.4517 Evaluate side-chains 237 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 195 time to evaluate : 0.325 ------------------------------------------------------------------------------- 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 350 TYR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 174 HIS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 623 SER Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain D residue 25 GLU 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 188 VAL Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 237 ARG Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 333 CYS Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 477 MET Chi-restraints excluded: chain E residue 505 LEU Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain E residue 525 LEU Chi-restraints excluded: chain E residue 543 ILE Chi-restraints excluded: chain E residue 623 SER Chi-restraints excluded: chain E residue 640 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 46 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 99 optimal weight: 0.6980 chunk 67 optimal weight: 0.7980 chunk 122 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 134 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN B 144 ASN ** B 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 21 GLN D 62 GLN E 144 ASN ** E 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 689 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.116769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.094553 restraints weight = 18479.713| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 3.44 r_work: 0.3144 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.9942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11398 Z= 0.147 Angle : 0.761 16.283 15570 Z= 0.361 Chirality : 0.045 0.216 1744 Planarity : 0.006 0.049 1990 Dihedral : 8.290 144.871 1579 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.18 % Favored : 91.68 % Rotamer: Outliers : 4.41 % Allowed : 28.10 % Favored : 67.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.23), residues: 1394 helix: 2.68 (0.23), residues: 496 sheet: -0.88 (0.33), residues: 210 loop : -1.90 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 279 TYR 0.013 0.001 TYR E 382 PHE 0.029 0.002 PHE E 312 TRP 0.012 0.001 TRP B 400 HIS 0.006 0.001 HIS A 26 Details of bonding type rmsd covalent geometry : bond 0.00345 (11398) covalent geometry : angle 0.76122 (15570) hydrogen bonds : bond 0.04367 ( 490) hydrogen bonds : angle 4.10556 ( 1398) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 203 time to evaluate : 0.358 Fit side-chains revert: symmetry clash REVERT: A 61 MET cc_start: 0.8884 (tpp) cc_final: 0.8266 (tpp) REVERT: A 94 TYR cc_start: 0.7967 (OUTLIER) cc_final: 0.7518 (m-80) REVERT: A 362 ILE cc_start: 0.9277 (tt) cc_final: 0.8830 (pt) REVERT: B 141 ILE cc_start: 0.9143 (mt) cc_final: 0.8906 (mp) REVERT: B 155 THR cc_start: 0.8399 (m) cc_final: 0.8109 (p) REVERT: B 237 ARG cc_start: 0.8189 (mtt180) cc_final: 0.7816 (mtm-85) REVERT: B 309 GLN cc_start: 0.8485 (tt0) cc_final: 0.8255 (mt0) REVERT: B 367 ASP cc_start: 0.7950 (OUTLIER) cc_final: 0.7694 (OUTLIER) REVERT: B 525 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8444 (tp) REVERT: B 618 THR cc_start: 0.9277 (m) cc_final: 0.9076 (t) REVERT: B 662 ARG cc_start: 0.8476 (tpp80) cc_final: 0.8048 (ttt-90) REVERT: D 172 LYS cc_start: 0.8707 (tppt) cc_final: 0.8310 (tmmt) REVERT: D 362 ILE cc_start: 0.9276 (tt) cc_final: 0.8860 (pt) REVERT: E 141 ILE cc_start: 0.8780 (mt) cc_final: 0.8554 (mp) REVERT: E 222 GLN cc_start: 0.8159 (pt0) cc_final: 0.7725 (pp30) REVERT: E 320 LEU cc_start: 0.7317 (OUTLIER) cc_final: 0.6889 (pt) REVERT: E 333 CYS cc_start: 0.8398 (OUTLIER) cc_final: 0.8148 (m) REVERT: E 377 ASP cc_start: 0.8381 (t70) cc_final: 0.7985 (t0) REVERT: E 394 VAL cc_start: 0.8860 (OUTLIER) cc_final: 0.8619 (m) REVERT: E 477 MET cc_start: 0.9069 (OUTLIER) cc_final: 0.8811 (mtm) REVERT: E 525 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8609 (tp) REVERT: E 534 TYR cc_start: 0.8123 (m-80) cc_final: 0.7549 (m-80) REVERT: E 554 GLU cc_start: 0.8650 (tt0) cc_final: 0.8135 (mt-10) REVERT: E 662 ARG cc_start: 0.8611 (tpp80) cc_final: 0.8117 (ttt-90) outliers start: 52 outliers final: 34 residues processed: 242 average time/residue: 0.3801 time to fit residues: 102.7147 Evaluate side-chains 225 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 184 time to evaluate : 0.397 ------------------------------------------------------------------------------- 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 156 ILE Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 174 HIS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 651 THR 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 188 VAL Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 333 CYS Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 477 MET Chi-restraints excluded: chain E residue 505 LEU Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain E residue 521 GLU Chi-restraints excluded: chain E residue 525 LEU Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain E residue 543 ILE Chi-restraints excluded: chain E residue 640 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 104 optimal weight: 0.9990 chunk 77 optimal weight: 8.9990 chunk 79 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 110 optimal weight: 0.1980 chunk 34 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN ** A 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 ASN ** B 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 21 GLN ** D 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 533 GLN E 689 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.115720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.093895 restraints weight = 18247.481| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 3.44 r_work: 0.3163 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 1.0046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 11398 Z= 0.145 Angle : 0.773 15.235 15570 Z= 0.366 Chirality : 0.044 0.294 1744 Planarity : 0.006 0.051 1990 Dihedral : 8.252 144.043 1579 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.89 % Favored : 91.97 % Rotamer: Outliers : 4.16 % Allowed : 29.12 % Favored : 66.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.23), residues: 1394 helix: 2.66 (0.23), residues: 496 sheet: -0.88 (0.33), residues: 210 loop : -1.79 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 279 TYR 0.034 0.002 TYR E 382 PHE 0.027 0.002 PHE A 107 TRP 0.010 0.001 TRP E 214 HIS 0.009 0.001 HIS D 68 Details of bonding type rmsd covalent geometry : bond 0.00346 (11398) covalent geometry : angle 0.77312 (15570) hydrogen bonds : bond 0.04256 ( 490) hydrogen bonds : angle 4.09001 ( 1398) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 190 time to evaluate : 0.428 Fit side-chains revert: symmetry clash REVERT: A 94 TYR cc_start: 0.7915 (OUTLIER) cc_final: 0.7429 (m-80) REVERT: A 362 ILE cc_start: 0.9255 (tt) cc_final: 0.8836 (pt) REVERT: B 141 ILE cc_start: 0.9142 (mt) cc_final: 0.8913 (mp) REVERT: B 155 THR cc_start: 0.8321 (m) cc_final: 0.8055 (p) REVERT: B 237 ARG cc_start: 0.8210 (mtt180) cc_final: 0.7917 (ttp-110) REVERT: B 309 GLN cc_start: 0.8529 (tt0) cc_final: 0.8302 (mt0) REVERT: B 367 ASP cc_start: 0.7950 (OUTLIER) cc_final: 0.7703 (OUTLIER) REVERT: B 525 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8467 (tp) REVERT: B 554 GLU cc_start: 0.8452 (tt0) cc_final: 0.8097 (mt-10) REVERT: B 662 ARG cc_start: 0.8491 (tpp80) cc_final: 0.8074 (ttt-90) REVERT: D 172 LYS cc_start: 0.8677 (tppt) cc_final: 0.8294 (tmmt) REVERT: D 362 ILE cc_start: 0.9246 (tt) cc_final: 0.8855 (pt) REVERT: E 141 ILE cc_start: 0.8784 (mt) cc_final: 0.8551 (mp) REVERT: E 222 GLN cc_start: 0.8140 (pt0) cc_final: 0.7663 (pp30) REVERT: E 333 CYS cc_start: 0.8406 (OUTLIER) cc_final: 0.8190 (m) REVERT: E 394 VAL cc_start: 0.8883 (OUTLIER) cc_final: 0.8664 (m) REVERT: E 477 MET cc_start: 0.9032 (OUTLIER) cc_final: 0.8784 (mtm) REVERT: E 525 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8569 (tp) REVERT: E 534 TYR cc_start: 0.8141 (m-80) cc_final: 0.7553 (m-80) REVERT: E 554 GLU cc_start: 0.8653 (tt0) cc_final: 0.8133 (mt-10) REVERT: E 662 ARG cc_start: 0.8605 (tpp80) cc_final: 0.7965 (ttp80) outliers start: 49 outliers final: 36 residues processed: 226 average time/residue: 0.3694 time to fit residues: 93.3161 Evaluate side-chains 230 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 188 time to evaluate : 0.371 ------------------------------------------------------------------------------- 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 144 ASN Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 174 HIS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 651 THR 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 188 VAL Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 333 CYS Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 477 MET Chi-restraints excluded: chain E residue 505 LEU Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain E residue 525 LEU Chi-restraints excluded: chain E residue 543 ILE Chi-restraints excluded: chain E residue 640 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 90 optimal weight: 0.0270 chunk 120 optimal weight: 0.8980 chunk 18 optimal weight: 9.9990 chunk 75 optimal weight: 0.7980 chunk 50 optimal weight: 0.3980 chunk 118 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 21 optimal weight: 0.0570 chunk 35 optimal weight: 2.9990 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN ** A 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 ASN B 327 ASN ** B 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 21 GLN ** D 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 309 GLN E 533 GLN E 689 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.117270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.095382 restraints weight = 18375.871| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 3.44 r_work: 0.3182 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 1.0178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 11398 Z= 0.134 Angle : 0.763 14.881 15570 Z= 0.362 Chirality : 0.044 0.252 1744 Planarity : 0.006 0.049 1990 Dihedral : 8.149 143.104 1579 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.82 % Favored : 92.04 % Rotamer: Outliers : 4.07 % Allowed : 29.20 % Favored : 66.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.24), residues: 1394 helix: 2.69 (0.23), residues: 496 sheet: -0.84 (0.34), residues: 210 loop : -1.68 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 279 TYR 0.030 0.002 TYR E 382 PHE 0.026 0.002 PHE D 107 TRP 0.012 0.001 TRP B 214 HIS 0.013 0.001 HIS D 68 Details of bonding type rmsd covalent geometry : bond 0.00312 (11398) covalent geometry : angle 0.76257 (15570) hydrogen bonds : bond 0.04007 ( 490) hydrogen bonds : angle 4.07014 ( 1398) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 203 time to evaluate : 0.434 Fit side-chains revert: symmetry clash REVERT: A 94 TYR cc_start: 0.7772 (OUTLIER) cc_final: 0.7324 (m-80) REVERT: A 362 ILE cc_start: 0.9257 (tt) cc_final: 0.8844 (pt) REVERT: B 141 ILE cc_start: 0.9123 (mt) cc_final: 0.8906 (mp) REVERT: B 155 THR cc_start: 0.8289 (m) cc_final: 0.8064 (p) REVERT: B 237 ARG cc_start: 0.8180 (mtt180) cc_final: 0.7948 (ttp-110) REVERT: B 309 GLN cc_start: 0.8515 (tt0) cc_final: 0.8245 (mt0) REVERT: B 367 ASP cc_start: 0.7919 (OUTLIER) cc_final: 0.7691 (OUTLIER) REVERT: B 525 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8416 (tp) REVERT: B 662 ARG cc_start: 0.8481 (tpp80) cc_final: 0.8050 (ttt-90) REVERT: D 172 LYS cc_start: 0.8645 (tppt) cc_final: 0.8254 (tmmt) REVERT: D 362 ILE cc_start: 0.9238 (tt) cc_final: 0.8867 (pt) REVERT: E 222 GLN cc_start: 0.8093 (pt0) cc_final: 0.7788 (pp30) REVERT: E 237 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.7725 (mtm-85) REVERT: E 377 ASP cc_start: 0.8374 (t70) cc_final: 0.8162 (t70) REVERT: E 394 VAL cc_start: 0.8874 (OUTLIER) cc_final: 0.8661 (m) REVERT: E 477 MET cc_start: 0.9029 (OUTLIER) cc_final: 0.8768 (mtm) REVERT: E 525 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8555 (tp) REVERT: E 534 TYR cc_start: 0.7995 (m-80) cc_final: 0.7422 (m-80) REVERT: E 554 GLU cc_start: 0.8644 (tt0) cc_final: 0.8112 (mt-10) REVERT: E 662 ARG cc_start: 0.8599 (tpp80) cc_final: 0.7973 (ttp80) outliers start: 48 outliers final: 29 residues processed: 240 average time/residue: 0.3864 time to fit residues: 103.5777 Evaluate side-chains 231 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 196 time to evaluate : 0.371 ------------------------------------------------------------------------------- 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 156 ILE Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 174 HIS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 640 LEU 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 188 VAL Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 237 ARG Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 477 MET Chi-restraints excluded: chain E residue 505 LEU Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain E residue 521 GLU Chi-restraints excluded: chain E residue 525 LEU Chi-restraints excluded: chain E residue 543 ILE Chi-restraints excluded: chain E residue 640 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 19 optimal weight: 0.7980 chunk 41 optimal weight: 7.9990 chunk 18 optimal weight: 7.9990 chunk 115 optimal weight: 1.9990 chunk 131 optimal weight: 0.0020 chunk 126 optimal weight: 0.0980 chunk 89 optimal weight: 3.9990 chunk 132 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN ** A 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 21 GLN D 62 GLN ** D 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 HIS E 327 ASN E 689 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.117569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.095516 restraints weight = 18198.131| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 3.45 r_work: 0.3189 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 1.0272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 11398 Z= 0.138 Angle : 0.773 14.378 15570 Z= 0.367 Chirality : 0.044 0.244 1744 Planarity : 0.006 0.047 1990 Dihedral : 8.077 142.191 1579 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.82 % Favored : 92.04 % Rotamer: Outliers : 3.48 % Allowed : 30.90 % Favored : 65.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.24), residues: 1394 helix: 2.70 (0.23), residues: 496 sheet: -0.54 (0.35), residues: 210 loop : -1.66 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 279 TYR 0.027 0.002 TYR E 382 PHE 0.027 0.002 PHE D 107 TRP 0.011 0.001 TRP B 400 HIS 0.015 0.001 HIS D 68 Details of bonding type rmsd covalent geometry : bond 0.00330 (11398) covalent geometry : angle 0.77340 (15570) hydrogen bonds : bond 0.03908 ( 490) hydrogen bonds : angle 4.05261 ( 1398) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3277.03 seconds wall clock time: 56 minutes 30.25 seconds (3390.25 seconds total)