Starting phenix.real_space_refine on Fri Sep 11 19:31:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6of3_20041/09_2026/6of3_20041.cif Found real_map, /net/cci-nas-00/data/ceres_data/6of3_20041/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6of3_20041/09_2026/6of3_20041.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6of3_20041/09_2026/6of3_20041.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6of3_20041/09_2026/6of3_20041.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6of3_20041/09_2026/6of3_20041.map" model { file = "/net/cci-nas-00/data/ceres_data/6of3_20041/09_2026/6of3_20041.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6of3_20041/09_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-2.2.1-6174/lib/python3.11/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: 4.50, per 1000 atoms: 0.41 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: 0.90 Conformation dependent library (CDL) restraints added in 484.5 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: 0.32 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: 1.93 Time building geometry restraints manager: 1.22 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: 6611 33.07 - 66.13: 169 66.13 - 99.20: 2 99.20 - 132.26: 0 132.26 - 165.33: 2 Dihedral angle restraints: 6784 sinusoidal: 2666 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 6781 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: 0.840 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: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.980 Find NCS groups from input model: 0.210 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:5.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6469 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 : 14.696 165.331 4116 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/Z covalent geometry : bond 0.00810 / 0.38 (11398) covalent geometry : angle 1.59035 / 0.89 (15570) hydrogen bonds : bond 0.19908 / 13.50 ( 490) hydrogen bonds : angle 6.07747 / 4.52 ( 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 : 0.414 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: 0.4780 time to fit residues: 195.1884 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 : 0.409 ------------------------------------------------------------------------------- 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... 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 = 0.3624 r_free = 0.3624 target = 0.115875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.095096 restraints weight = 18485.629| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 3.34 r_work: 0.3187 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.3892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 11398 Z= 0.191 Angle : 0.958 13.525 15570 Z= 0.469 Chirality : 0.049 0.175 1744 Planarity : 0.007 0.063 1990 Dihedral : 9.588 161.941 1566 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.86 % Allowed : 9.11 % Favored : 90.03 % Rotamer: Outliers : 5.77 % Allowed : 16.89 % Favored : 77.33 % 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: -1.08 (0.23), residues: 1394 helix: 2.26 (0.23), residues: 452 sheet: -0.80 (0.36), residues: 192 loop : -2.80 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 662 TYR 0.021 0.002 TYR E 685 PHE 0.038 0.003 PHE E 139 TRP 0.024 0.002 TRP B 722 HIS 0.013 0.002 HIS B 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.19 (11398) covalent geometry : angle 0.95835 / 0.47 (15570) hydrogen bonds : bond 0.05604 / 3.91 ( 490) hydrogen bonds : angle 4.97088 / 3.76 ( 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 318 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 250 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 141 ILE cc_start: 0.8590 (mt) cc_final: 0.8350 (mp) REVERT: B 318 VAL cc_start: 0.7356 (m) cc_final: 0.7046 (m) REVERT: B 364 PRO cc_start: 0.5819 (Cg_exo) cc_final: 0.5600 (Cg_endo) REVERT: B 479 MET cc_start: 0.7705 (tpp) cc_final: 0.6866 (tpt) REVERT: D 94 TYR cc_start: 0.5249 (OUTLIER) cc_final: 0.4984 (m-80) REVERT: D 172 LYS cc_start: 0.7396 (OUTLIER) cc_final: 0.6935 (ttmt) REVERT: E 121 PHE cc_start: 0.6387 (m-80) cc_final: 0.6142 (t80) REVERT: E 367 ASP cc_start: 0.6649 (t0) cc_final: 0.6241 (m-30) REVERT: E 537 GLU cc_start: 0.8194 (mp0) cc_final: 0.7917 (mp0) REVERT: E 546 MET cc_start: 0.7645 (mmm) cc_final: 0.7398 (mpp) REVERT: E 559 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7786 (tp) REVERT: E 644 ASN cc_start: 0.6472 (OUTLIER) cc_final: 0.6189 (m-40) REVERT: E 672 LYS cc_start: 0.8321 (mmmm) cc_final: 0.8101 (mmmt) outliers start: 68 outliers final: 23 residues processed: 289 average time/residue: 0.4159 time to fit residues: 133.8990 Evaluate side-chains 234 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 207 time to evaluate : 0.442 ------------------------------------------------------------------------------- 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 506 THR 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 474 LEU Chi-restraints excluded: chain E residue 559 LEU 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: 0.9990 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: 3.9990 chunk 54 optimal weight: 0.0040 chunk 98 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 25 optimal weight: 0.3980 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 171 HIS B 357 HIS B 644 ASN B 689 ASN D 21 GLN D 26 HIS E 283 ASN E 357 HIS E 532 HIS E 689 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.117026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.096136 restraints weight = 18631.069| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 3.37 r_work: 0.3210 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.5063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 11398 Z= 0.166 Angle : 0.849 12.528 15570 Z= 0.412 Chirality : 0.046 0.182 1744 Planarity : 0.006 0.059 1990 Dihedral : 8.866 159.160 1561 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.90 % Favored : 90.82 % Rotamer: Outliers : 6.11 % Allowed : 19.52 % Favored : 74.36 % 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: -0.60 (0.23), residues: 1394 helix: 2.45 (0.23), residues: 486 sheet: -0.88 (0.33), residues: 210 loop : -2.50 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 205 TYR 0.019 0.002 TYR E 225 PHE 0.030 0.003 PHE A 107 TRP 0.016 0.001 TRP E 500 HIS 0.007 0.001 HIS B 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.17 (11398) covalent geometry : angle 0.84896 / 0.41 (15570) hydrogen bonds : bond 0.04960 / 3.43 ( 490) hydrogen bonds : angle 4.54492 / 3.42 ( 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 300 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 228 time to evaluate : 0.422 Fit side-chains REVERT: A 21 GLN cc_start: 0.7427 (OUTLIER) cc_final: 0.7138 (tt0) REVERT: B 141 ILE cc_start: 0.8848 (mt) cc_final: 0.8577 (mp) REVERT: B 479 MET cc_start: 0.8232 (tpp) cc_final: 0.7311 (tpt) REVERT: B 567 ASP cc_start: 0.6011 (OUTLIER) cc_final: 0.5437 (t0) REVERT: B 672 LYS cc_start: 0.8495 (mmmm) cc_final: 0.8127 (mmmt) REVERT: D 21 GLN cc_start: 0.7251 (OUTLIER) cc_final: 0.6979 (tt0) REVERT: D 94 TYR cc_start: 0.5675 (OUTLIER) cc_final: 0.5438 (m-80) REVERT: D 172 LYS cc_start: 0.7530 (tppt) cc_final: 0.6985 (ttmt) REVERT: E 477 MET cc_start: 0.8146 (tpp) cc_final: 0.7807 (mmp) REVERT: E 479 MET cc_start: 0.7850 (tpt) cc_final: 0.7501 (tpt) REVERT: E 525 LEU cc_start: 0.6749 (OUTLIER) cc_final: 0.6411 (tp) REVERT: E 537 GLU cc_start: 0.8201 (mp0) cc_final: 0.7904 (mp0) REVERT: E 567 ASP cc_start: 0.5904 (OUTLIER) cc_final: 0.5431 (t0) REVERT: E 672 LYS cc_start: 0.8666 (mmmm) cc_final: 0.8408 (mmmt) outliers start: 72 outliers final: 26 residues processed: 278 average time/residue: 0.4203 time to fit residues: 130.2162 Evaluate side-chains 238 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 206 time to evaluate : 0.412 ------------------------------------------------------------------------------- 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 174 HIS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 229 ASP 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 27 THR Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 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 363 THR Chi-restraints excluded: chain E residue 474 LEU Chi-restraints excluded: chain E residue 506 THR 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: 1.9990 chunk 101 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 133 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 74 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 GLN A 62 GLN B 118 ASN B 283 ASN ** B 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 ASN D 26 HIS D 68 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.119177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.096996 restraints weight = 18256.025| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 3.57 r_work: 0.3211 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.8269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 11398 Z= 0.289 Angle : 0.961 14.986 15570 Z= 0.480 Chirality : 0.051 0.236 1744 Planarity : 0.007 0.059 1990 Dihedral : 8.791 151.804 1557 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.29 % Allowed : 9.76 % Favored : 89.96 % Rotamer: Outliers : 7.64 % Allowed : 20.03 % Favored : 72.33 % 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: -0.95 (0.22), residues: 1394 helix: 2.10 (0.23), residues: 470 sheet: -0.73 (0.36), residues: 200 loop : -2.65 (0.20), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 522 TYR 0.028 0.003 TYR D 23 PHE 0.040 0.003 PHE A 107 TRP 0.030 0.002 TRP B 500 HIS 0.013 0.002 HIS E 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00683 / 0.29 (11398) covalent geometry : angle 0.96103 / 0.48 (15570) hydrogen bonds : bond 0.06581 / 4.56 ( 490) hydrogen bonds : angle 4.79375 / 3.59 ( 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 340 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 250 time to evaluate : 0.432 Fit side-chains revert: symmetry clash REVERT: A 61 MET cc_start: 0.9033 (mmm) cc_final: 0.8801 (tpp) REVERT: B 141 ILE cc_start: 0.9154 (mt) cc_final: 0.8848 (mp) REVERT: B 183 THR cc_start: 0.8424 (p) cc_final: 0.8202 (t) REVERT: B 320 LEU cc_start: 0.7652 (pt) cc_final: 0.7135 (pp) REVERT: B 367 ASP cc_start: 0.8054 (t0) cc_final: 0.7672 (m-30) REVERT: B 396 ASN cc_start: 0.8348 (p0) cc_final: 0.7838 (p0) REVERT: B 525 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8162 (tp) REVERT: D 21 GLN cc_start: 0.8164 (OUTLIER) cc_final: 0.7898 (tt0) REVERT: D 23 TYR cc_start: 0.8410 (m-80) cc_final: 0.7668 (m-80) REVERT: D 72 SER cc_start: 0.8505 (t) cc_final: 0.8250 (p) REVERT: D 153 THR cc_start: 0.8491 (m) cc_final: 0.8212 (p) REVERT: D 172 LYS cc_start: 0.8671 (tppt) cc_final: 0.8260 (ttmt) REVERT: E 237 ARG cc_start: 0.7850 (ptp-170) cc_final: 0.7577 (mtm-85) REVERT: E 266 ILE cc_start: 0.8539 (pt) cc_final: 0.8292 (pp) REVERT: E 420 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7336 (mm-30) REVERT: E 424 MET cc_start: 0.8588 (mmm) cc_final: 0.7041 (mtm) REVERT: E 477 MET cc_start: 0.8875 (OUTLIER) cc_final: 0.8585 (mtm) REVERT: E 525 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8161 (tp) REVERT: E 618 THR cc_start: 0.9256 (m) cc_final: 0.9004 (t) REVERT: E 625 GLN cc_start: 0.7887 (OUTLIER) cc_final: 0.7574 (mt0) REVERT: E 672 LYS cc_start: 0.8881 (mmmm) cc_final: 0.8605 (mmmt) outliers start: 90 outliers final: 41 residues processed: 307 average time/residue: 0.4037 time to fit residues: 138.4178 Evaluate side-chains 236 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 190 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 192 LEU Chi-restraints excluded: chain B residue 253 LEU 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 445 THR Chi-restraints excluded: chain B residue 448 PHE Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 567 ASP Chi-restraints excluded: chain B residue 623 SER Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain D residue 21 GLN Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 360 ILE 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 188 VAL Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 226 THR 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 367 ASP Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 445 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 623 SER Chi-restraints excluded: chain E residue 625 GLN Chi-restraints excluded: chain E residue 635 ILE Chi-restraints excluded: chain E residue 639 SER Chi-restraints excluded: chain E residue 720 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 126 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 56 optimal weight: 0.9980 chunk 89 optimal weight: 5.9990 chunk 136 optimal weight: 0.0030 chunk 129 optimal weight: 3.9990 chunk 130 optimal weight: 0.0050 chunk 36 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 overall best weight: 1.4008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 GLN ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 HIS B 357 HIS ** B 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 ASN D 26 HIS ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 HIS ** E 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 357 HIS ** E 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.115586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.093558 restraints weight = 18520.252| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 3.45 r_work: 0.3129 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.8874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 11398 Z= 0.196 Angle : 0.832 14.985 15570 Z= 0.402 Chirality : 0.047 0.409 1744 Planarity : 0.006 0.057 1990 Dihedral : 8.667 151.490 1557 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.54 % Favored : 91.32 % Rotamer: Outliers : 7.05 % Allowed : 23.94 % Favored : 69.02 % 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: -0.60 (0.22), residues: 1394 helix: 2.37 (0.23), residues: 484 sheet: -0.85 (0.35), residues: 204 loop : -2.42 (0.21), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 289 TYR 0.016 0.002 TYR B 382 PHE 0.029 0.003 PHE A 107 TRP 0.013 0.001 TRP E 500 HIS 0.009 0.001 HIS E 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.20 (11398) covalent geometry : angle 0.83191 / 0.40 (15570) hydrogen bonds : bond 0.05445 / 3.77 ( 490) hydrogen bonds : angle 4.52005 / 3.41 ( 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 291 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 208 time to evaluate : 0.408 Fit side-chains REVERT: A 94 TYR cc_start: 0.8166 (OUTLIER) cc_final: 0.7857 (m-80) REVERT: A 165 TRP cc_start: 0.8610 (t60) cc_final: 0.8349 (t60) REVERT: B 141 ILE cc_start: 0.9189 (mt) cc_final: 0.8925 (mp) REVERT: B 155 THR cc_start: 0.8344 (m) cc_final: 0.7880 (p) REVERT: B 237 ARG cc_start: 0.7933 (mtt180) cc_final: 0.7490 (mtm-85) REVERT: B 301 MET cc_start: 0.8487 (mtt) cc_final: 0.8232 (mtt) REVERT: B 367 ASP cc_start: 0.7870 (OUTLIER) cc_final: 0.7558 (m-30) REVERT: B 407 ASP cc_start: 0.8900 (t0) cc_final: 0.8633 (m-30) REVERT: B 525 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8331 (tp) REVERT: B 662 ARG cc_start: 0.8526 (tpp80) cc_final: 0.7878 (ttt-90) REVERT: D 23 TYR cc_start: 0.8362 (m-80) cc_final: 0.7792 (m-80) REVERT: D 72 SER cc_start: 0.8676 (t) cc_final: 0.8395 (p) REVERT: D 153 THR cc_start: 0.8443 (m) cc_final: 0.8180 (p) REVERT: D 172 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8343 (ttmt) REVERT: E 121 PHE cc_start: 0.7441 (m-80) cc_final: 0.7067 (t80) REVERT: E 142 LEU cc_start: 0.8116 (tp) cc_final: 0.7886 (tm) REVERT: E 222 GLN cc_start: 0.8246 (pt0) cc_final: 0.7864 (pp30) REVERT: E 309 GLN cc_start: 0.8480 (tt0) cc_final: 0.8275 (mt0) REVERT: E 382 TYR cc_start: 0.8111 (t80) cc_final: 0.7742 (t80) REVERT: E 407 ASP cc_start: 0.8808 (t0) cc_final: 0.8593 (m-30) REVERT: E 424 MET cc_start: 0.8639 (mmm) cc_final: 0.7007 (mtm) REVERT: E 525 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8389 (tp) REVERT: E 662 ARG cc_start: 0.8652 (tpp80) cc_final: 0.7979 (ttt-90) outliers start: 83 outliers final: 41 residues processed: 261 average time/residue: 0.3964 time to fit residues: 115.8876 Evaluate side-chains 237 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 191 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL 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 302 VAL Chi-restraints excluded: chain B residue 328 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 525 LEU Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain B residue 567 ASP Chi-restraints excluded: chain B residue 623 SER Chi-restraints excluded: chain B residue 644 ASN Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 720 VAL Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 172 LYS 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 353 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 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 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 639 SER Chi-restraints excluded: chain E residue 725 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 100 optimal weight: 6.9990 chunk 110 optimal weight: 0.6980 chunk 126 optimal weight: 0.0980 chunk 25 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 89 optimal weight: 8.9990 chunk 138 optimal weight: 0.4980 chunk 90 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 GLN B 144 ASN ** B 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 648 HIS D 21 GLN D 26 HIS E 144 ASN ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.116812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.094664 restraints weight = 18458.481| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 3.46 r_work: 0.3141 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.9191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 11398 Z= 0.153 Angle : 0.777 12.903 15570 Z= 0.374 Chirality : 0.045 0.343 1744 Planarity : 0.006 0.049 1990 Dihedral : 8.475 150.324 1557 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.61 % Favored : 91.25 % Rotamer: Outliers : 5.35 % Allowed : 25.55 % Favored : 69.10 % 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: -0.50 (0.23), residues: 1394 helix: 2.47 (0.23), residues: 488 sheet: -1.06 (0.33), residues: 222 loop : -2.32 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 128 TYR 0.017 0.001 TYR B 382 PHE 0.027 0.002 PHE E 312 TRP 0.011 0.001 TRP E 500 HIS 0.004 0.001 HIS B 532 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 (11398) covalent geometry : angle 0.77749 / 0.37 (15570) hydrogen bonds : bond 0.04784 / 3.32 ( 490) hydrogen bonds : angle 4.33444 / 3.26 ( 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 261 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 198 time to evaluate : 0.369 Fit side-chains REVERT: A 94 TYR cc_start: 0.8098 (OUTLIER) cc_final: 0.7700 (m-80) REVERT: A 165 TRP cc_start: 0.8511 (t60) cc_final: 0.8189 (t60) REVERT: B 141 ILE cc_start: 0.9152 (mt) cc_final: 0.8895 (mp) REVERT: B 155 THR cc_start: 0.8387 (m) cc_final: 0.7968 (p) REVERT: B 237 ARG cc_start: 0.8014 (mtt180) cc_final: 0.7573 (mtm-85) REVERT: B 301 MET cc_start: 0.8519 (mtt) cc_final: 0.8275 (mtt) REVERT: B 367 ASP cc_start: 0.7821 (OUTLIER) cc_final: 0.7545 (m-30) REVERT: B 407 ASP cc_start: 0.8912 (t0) cc_final: 0.8676 (m-30) REVERT: B 431 GLU cc_start: 0.8483 (pt0) cc_final: 0.8245 (tm-30) REVERT: B 525 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8363 (tp) REVERT: B 662 ARG cc_start: 0.8524 (tpp80) cc_final: 0.7978 (ttt-90) REVERT: D 72 SER cc_start: 0.8647 (t) cc_final: 0.8386 (p) REVERT: D 172 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8287 (ttmt) REVERT: D 349 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8926 (tt) REVERT: E 183 THR cc_start: 0.8241 (p) cc_final: 0.8012 (t) REVERT: E 222 GLN cc_start: 0.8222 (pt0) cc_final: 0.7840 (pp30) REVERT: E 424 MET cc_start: 0.8576 (mmm) cc_final: 0.7076 (mtm) REVERT: E 525 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8436 (tp) REVERT: E 662 ARG cc_start: 0.8602 (tpp80) cc_final: 0.7939 (ttp80) REVERT: E 664 ASP cc_start: 0.4659 (m-30) cc_final: 0.4233 (m-30) outliers start: 63 outliers final: 36 residues processed: 238 average time/residue: 0.4143 time to fit residues: 110.1128 Evaluate side-chains 232 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 190 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU 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 328 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 485 LEU 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 75 LEU Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 172 LYS Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 286 MET Chi-restraints excluded: chain E residue 353 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 425 SER Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain E residue 470 THR 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 639 SER Chi-restraints excluded: chain E residue 720 VAL Chi-restraints excluded: chain E residue 725 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 92 optimal weight: 7.9990 chunk 51 optimal weight: 0.6980 chunk 109 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 43 optimal weight: 0.9980 chunk 5 optimal weight: 0.0000 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 GLN ** B 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 21 GLN D 62 GLN D 143 GLN ** E 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 689 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.117727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.095407 restraints weight = 18319.139| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 3.45 r_work: 0.3157 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.9538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 11398 Z= 0.140 Angle : 0.761 14.034 15570 Z= 0.364 Chirality : 0.045 0.386 1744 Planarity : 0.006 0.048 1990 Dihedral : 8.344 149.764 1557 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.46 % Favored : 91.39 % Rotamer: Outliers : 5.26 % Allowed : 26.49 % Favored : 68.25 % 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: -0.32 (0.23), residues: 1394 helix: 2.51 (0.23), residues: 498 sheet: -1.05 (0.32), residues: 222 loop : -2.16 (0.22), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 279 TYR 0.021 0.002 TYR B 626 PHE 0.029 0.002 PHE E 312 TRP 0.008 0.001 TRP B 400 HIS 0.005 0.001 HIS D 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (11398) covalent geometry : angle 0.76082 / 0.36 (15570) hydrogen bonds : bond 0.04308 / 2.98 ( 490) hydrogen bonds : angle 4.19297 / 3.15 ( 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 257 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 195 time to evaluate : 0.603 Fit side-chains REVERT: A 362 ILE cc_start: 0.9264 (tt) cc_final: 0.8807 (pt) REVERT: B 141 ILE cc_start: 0.9148 (mt) cc_final: 0.8914 (mp) REVERT: B 155 THR cc_start: 0.8392 (m) cc_final: 0.8103 (p) REVERT: B 237 ARG cc_start: 0.8066 (mtt180) cc_final: 0.7639 (mtm-85) REVERT: B 320 LEU cc_start: 0.7261 (pt) cc_final: 0.6648 (pp) REVERT: B 367 ASP cc_start: 0.7814 (OUTLIER) cc_final: 0.7577 (m-30) REVERT: B 394 VAL cc_start: 0.8852 (OUTLIER) cc_final: 0.8602 (m) REVERT: B 525 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8408 (tp) REVERT: B 662 ARG cc_start: 0.8550 (tpp80) cc_final: 0.8123 (ttt-90) REVERT: D 72 SER cc_start: 0.8691 (t) cc_final: 0.8452 (p) REVERT: D 172 LYS cc_start: 0.8622 (tppt) cc_final: 0.8273 (ttmt) REVERT: E 121 PHE cc_start: 0.7259 (OUTLIER) cc_final: 0.6919 (t80) REVERT: E 222 GLN cc_start: 0.8259 (pt0) cc_final: 0.7666 (pp30) REVERT: E 237 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.7712 (mtm-85) REVERT: E 320 LEU cc_start: 0.7353 (pt) cc_final: 0.6819 (pp) REVERT: E 353 THR cc_start: 0.8652 (OUTLIER) cc_final: 0.8427 (p) REVERT: E 377 ASP cc_start: 0.8365 (t70) cc_final: 0.8027 (t0) REVERT: E 394 VAL cc_start: 0.8848 (OUTLIER) cc_final: 0.8605 (m) REVERT: E 424 MET cc_start: 0.8543 (mmm) cc_final: 0.7128 (mtm) REVERT: E 525 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8520 (tp) REVERT: E 534 TYR cc_start: 0.8001 (m-80) cc_final: 0.7483 (m-80) REVERT: E 556 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8471 (tmmm) REVERT: E 662 ARG cc_start: 0.8581 (tpp80) cc_final: 0.8121 (ttt-90) outliers start: 62 outliers final: 30 residues processed: 238 average time/residue: 0.3953 time to fit residues: 105.7095 Evaluate side-chains 219 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 180 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 328 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 525 LEU Chi-restraints excluded: chain B residue 567 ASP Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain E residue 121 PHE 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 353 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 425 SER Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain E residue 470 THR 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 556 LYS Chi-restraints excluded: chain E residue 559 LEU Chi-restraints excluded: chain E residue 623 SER Chi-restraints excluded: chain E residue 639 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: 4.9990 chunk 42 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 GLN ** A 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 HIS B 144 ASN ** B 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 21 GLN D 62 GLN ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 151 GLN ** 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 = 0.3608 r_free = 0.3608 target = 0.116416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.094147 restraints weight = 18398.648| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 3.43 r_work: 0.3143 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.9928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11398 Z= 0.151 Angle : 0.773 13.420 15570 Z= 0.368 Chirality : 0.046 0.388 1744 Planarity : 0.006 0.047 1990 Dihedral : 8.254 149.309 1557 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.68 % Favored : 91.18 % Rotamer: Outliers : 4.84 % Allowed : 27.59 % Favored : 67.57 % 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: 2.49 (0.23), residues: 498 sheet: -1.06 (0.32), residues: 220 loop : -2.05 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 279 TYR 0.029 0.002 TYR B 382 PHE 0.027 0.002 PHE A 107 TRP 0.008 0.001 TRP B 169 HIS 0.009 0.001 HIS A 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (11398) covalent geometry : angle 0.77257 / 0.37 (15570) hydrogen bonds : bond 0.04567 / 3.16 ( 490) hydrogen bonds : angle 4.17546 / 3.14 ( 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 245 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 188 time to evaluate : 0.424 Fit side-chains REVERT: A 94 TYR cc_start: 0.8114 (OUTLIER) cc_final: 0.7567 (m-80) REVERT: A 362 ILE cc_start: 0.9244 (tt) cc_final: 0.8819 (pt) REVERT: B 141 ILE cc_start: 0.9166 (mt) cc_final: 0.8917 (mp) REVERT: B 155 THR cc_start: 0.8419 (m) cc_final: 0.8074 (p) REVERT: B 237 ARG cc_start: 0.8221 (mtt180) cc_final: 0.7796 (mtm-85) REVERT: B 367 ASP cc_start: 0.7956 (OUTLIER) cc_final: 0.7742 (m-30) REVERT: B 525 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8439 (tp) REVERT: B 556 LYS cc_start: 0.8870 (OUTLIER) cc_final: 0.8539 (tmmm) REVERT: B 662 ARG cc_start: 0.8502 (tpp80) cc_final: 0.8096 (ttt-90) REVERT: D 72 SER cc_start: 0.8692 (t) cc_final: 0.8462 (p) REVERT: D 124 MET cc_start: 0.7679 (ppp) cc_final: 0.7410 (tmm) REVERT: D 172 LYS cc_start: 0.8692 (tppt) cc_final: 0.8307 (tmmt) REVERT: D 362 ILE cc_start: 0.9262 (tt) cc_final: 0.8851 (pt) REVERT: E 121 PHE cc_start: 0.6926 (OUTLIER) cc_final: 0.6560 (t80) REVERT: E 222 GLN cc_start: 0.8158 (pt0) cc_final: 0.7884 (pp30) REVERT: E 251 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7579 (tp30) REVERT: E 320 LEU cc_start: 0.7391 (pt) cc_final: 0.6817 (pp) REVERT: E 353 THR cc_start: 0.8703 (OUTLIER) cc_final: 0.8473 (p) REVERT: E 377 ASP cc_start: 0.8457 (t70) cc_final: 0.8114 (t0) REVERT: E 394 VAL cc_start: 0.8865 (OUTLIER) cc_final: 0.8629 (m) REVERT: E 424 MET cc_start: 0.8616 (mmm) cc_final: 0.7297 (mtm) REVERT: E 525 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8539 (tp) REVERT: E 534 TYR cc_start: 0.8127 (m-80) cc_final: 0.7553 (m-80) REVERT: E 662 ARG cc_start: 0.8555 (tpp80) cc_final: 0.8104 (ttt-90) outliers start: 57 outliers final: 31 residues processed: 227 average time/residue: 0.4182 time to fit residues: 105.9673 Evaluate side-chains 215 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 175 time to evaluate : 0.441 ------------------------------------------------------------------------------- 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 287 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 328 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 525 LEU Chi-restraints excluded: chain B residue 556 LYS Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain E residue 121 PHE Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 251 GLU Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 353 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 513 VAL Chi-restraints excluded: chain E residue 525 LEU Chi-restraints excluded: chain E residue 537 GLU Chi-restraints excluded: chain E residue 559 LEU Chi-restraints excluded: chain E residue 639 SER 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: 0.9980 chunk 59 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 79 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 110 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 100 optimal weight: 8.9990 chunk 115 optimal weight: 1.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 GLN ** A 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 ASN ** B 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 648 HIS D 21 GLN D 62 GLN ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 309 GLN ** 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 = 0.3565 r_free = 0.3565 target = 0.112548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.090631 restraints weight = 18302.032| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 3.39 r_work: 0.3119 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 1.0339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 11398 Z= 0.202 Angle : 0.806 12.912 15570 Z= 0.391 Chirality : 0.047 0.367 1744 Planarity : 0.006 0.050 1990 Dihedral : 8.265 149.711 1557 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.61 % Favored : 91.25 % Rotamer: Outliers : 4.75 % Allowed : 28.18 % Favored : 67.06 % 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: -0.29 (0.23), residues: 1394 helix: 2.50 (0.23), residues: 484 sheet: -1.12 (0.32), residues: 220 loop : -1.97 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 279 TYR 0.031 0.002 TYR E 382 PHE 0.027 0.002 PHE A 107 TRP 0.011 0.001 TRP B 169 HIS 0.010 0.001 HIS A 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.20 (11398) covalent geometry : angle 0.80614 / 0.39 (15570) hydrogen bonds : bond 0.05288 / 3.67 ( 490) hydrogen bonds : angle 4.27239 / 3.21 ( 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 246 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 190 time to evaluate : 0.432 Fit side-chains REVERT: A 94 TYR cc_start: 0.8126 (OUTLIER) cc_final: 0.7544 (m-80) REVERT: A 362 ILE cc_start: 0.9211 (tt) cc_final: 0.8799 (pt) REVERT: B 141 ILE cc_start: 0.9146 (mt) cc_final: 0.8888 (mp) REVERT: B 237 ARG cc_start: 0.8283 (mtt180) cc_final: 0.7875 (mtm-85) REVERT: B 251 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7631 (tp30) REVERT: B 367 ASP cc_start: 0.8175 (OUTLIER) cc_final: 0.7833 (m-30) REVERT: B 525 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8477 (tp) REVERT: B 556 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8571 (tmmm) REVERT: B 662 ARG cc_start: 0.8529 (tpp80) cc_final: 0.8083 (ttt-90) REVERT: D 172 LYS cc_start: 0.8879 (tppt) cc_final: 0.8465 (tmmt) REVERT: D 362 ILE cc_start: 0.9219 (tt) cc_final: 0.8841 (pt) REVERT: E 121 PHE cc_start: 0.6838 (OUTLIER) cc_final: 0.6472 (t80) REVERT: E 222 GLN cc_start: 0.8218 (pt0) cc_final: 0.7785 (pp30) REVERT: E 251 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7655 (tp30) REVERT: E 321 THR cc_start: 0.8793 (m) cc_final: 0.8576 (p) REVERT: E 377 ASP cc_start: 0.8487 (t70) cc_final: 0.8165 (t0) REVERT: E 424 MET cc_start: 0.8751 (mmm) cc_final: 0.7376 (mtm) REVERT: E 525 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8564 (tp) REVERT: E 534 TYR cc_start: 0.8134 (m-80) cc_final: 0.7496 (m-80) REVERT: E 556 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8541 (tmmm) REVERT: E 662 ARG cc_start: 0.8636 (tpp80) cc_final: 0.7997 (ttp80) outliers start: 56 outliers final: 32 residues processed: 230 average time/residue: 0.4466 time to fit residues: 113.7716 Evaluate side-chains 222 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 181 time to evaluate : 0.422 ------------------------------------------------------------------------------- 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 174 HIS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 328 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 446 ILE Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 556 LYS Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain E residue 121 PHE Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 251 GLU Chi-restraints excluded: chain E residue 353 THR Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 367 ASP 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 513 VAL Chi-restraints excluded: chain E residue 525 LEU Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain E residue 556 LYS Chi-restraints excluded: chain E residue 559 LEU Chi-restraints excluded: chain E residue 639 SER 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: 0.7980 chunk 120 optimal weight: 4.9990 chunk 18 optimal weight: 8.9990 chunk 75 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 118 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 130 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 GLN ** A 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 HIS ** B 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 648 HIS D 21 GLN ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 143 GLN ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.114126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.092245 restraints weight = 18424.237| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 3.40 r_work: 0.3123 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 1.0373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 11398 Z= 0.204 Angle : 0.992 59.197 15570 Z= 0.538 Chirality : 0.046 0.359 1744 Planarity : 0.006 0.049 1990 Dihedral : 8.276 149.768 1557 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.68 % Favored : 91.18 % Rotamer: Outliers : 3.65 % Allowed : 30.56 % Favored : 65.79 % 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: -0.29 (0.23), residues: 1394 helix: 2.49 (0.23), residues: 484 sheet: -1.12 (0.32), residues: 220 loop : -1.96 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 279 TYR 0.032 0.002 TYR B 382 PHE 0.026 0.002 PHE A 107 TRP 0.021 0.001 TRP B 297 HIS 0.010 0.001 HIS A 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.20 (11398) covalent geometry : angle 0.99154 / 0.54 (15570) hydrogen bonds : bond 0.05297 / 3.67 ( 490) hydrogen bonds : angle 4.27207 / 3.21 ( 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 224 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 181 time to evaluate : 0.444 Fit side-chains REVERT: A 94 TYR cc_start: 0.8120 (OUTLIER) cc_final: 0.7542 (m-80) REVERT: A 362 ILE cc_start: 0.9193 (tt) cc_final: 0.8797 (pt) REVERT: B 141 ILE cc_start: 0.9144 (mt) cc_final: 0.8885 (mp) REVERT: B 144 ASN cc_start: 0.7983 (OUTLIER) cc_final: 0.7563 (p0) REVERT: B 237 ARG cc_start: 0.8260 (mtt180) cc_final: 0.7868 (mtm-85) REVERT: B 367 ASP cc_start: 0.8158 (OUTLIER) cc_final: 0.7814 (m-30) REVERT: B 525 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8472 (tp) REVERT: B 556 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8568 (tmmm) REVERT: B 662 ARG cc_start: 0.8504 (tpp80) cc_final: 0.8070 (ttt-90) REVERT: D 172 LYS cc_start: 0.8880 (tppt) cc_final: 0.8461 (tmmt) REVERT: D 362 ILE cc_start: 0.9217 (tt) cc_final: 0.8837 (pt) REVERT: E 121 PHE cc_start: 0.6833 (OUTLIER) cc_final: 0.6459 (t80) REVERT: E 222 GLN cc_start: 0.8222 (pt0) cc_final: 0.7789 (pp30) REVERT: E 251 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7659 (tp30) REVERT: E 321 THR cc_start: 0.8795 (m) cc_final: 0.8581 (p) REVERT: E 377 ASP cc_start: 0.8485 (t70) cc_final: 0.8163 (t0) REVERT: E 424 MET cc_start: 0.8751 (mmm) cc_final: 0.7372 (mtm) REVERT: E 525 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8563 (tp) REVERT: E 534 TYR cc_start: 0.8123 (m-80) cc_final: 0.7423 (m-80) REVERT: E 556 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8538 (tmmm) REVERT: E 662 ARG cc_start: 0.8615 (tpp80) cc_final: 0.7982 (ttp80) outliers start: 43 outliers final: 32 residues processed: 212 average time/residue: 0.4292 time to fit residues: 101.2589 Evaluate side-chains 220 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 179 time to evaluate : 0.432 ------------------------------------------------------------------------------- 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 174 HIS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 328 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 446 ILE Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 556 LYS Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain E residue 121 PHE Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 251 GLU Chi-restraints excluded: chain E residue 353 THR Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 367 ASP 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 513 VAL Chi-restraints excluded: chain E residue 525 LEU Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain E residue 556 LYS Chi-restraints excluded: chain E residue 559 LEU Chi-restraints excluded: chain E residue 639 SER 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: 8.9990 chunk 41 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 chunk 115 optimal weight: 0.8980 chunk 131 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 89 optimal weight: 10.0000 chunk 132 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 GLN ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 21 GLN ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.114507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.092722 restraints weight = 18236.045| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 3.38 r_work: 0.3118 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 1.0386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 11398 Z= 0.204 Angle : 0.992 59.197 15570 Z= 0.538 Chirality : 0.046 0.359 1744 Planarity : 0.006 0.049 1990 Dihedral : 8.276 149.768 1557 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.68 % Favored : 91.18 % Rotamer: Outliers : 3.57 % Allowed : 30.90 % Favored : 65.53 % 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: -0.29 (0.23), residues: 1394 helix: 2.49 (0.23), residues: 484 sheet: -1.12 (0.32), residues: 220 loop : -1.96 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 279 TYR 0.032 0.002 TYR B 382 PHE 0.026 0.002 PHE A 107 TRP 0.021 0.001 TRP B 297 HIS 0.010 0.001 HIS A 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.20 (11398) covalent geometry : angle 0.99154 / 0.54 (15570) hydrogen bonds : bond 0.05297 / 3.67 ( 490) hydrogen bonds : angle 4.27207 / 3.21 ( 1398) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3366.33 seconds wall clock time: 58 minutes 23.36 seconds (3503.36 seconds total)