Starting phenix.real_space_refine on Wed Feb 4 04:43:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lue_63395/02_2026/9lue_63395_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lue_63395/02_2026/9lue_63395.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lue_63395/02_2026/9lue_63395_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lue_63395/02_2026/9lue_63395_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lue_63395/02_2026/9lue_63395.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lue_63395/02_2026/9lue_63395.map" } resolution = 3.03 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= -0.000 sd= 0.042 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: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 5501 2.51 5 N 1441 2.21 5 O 1703 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8693 Number of models: 1 Model: "" Number of chains: 8 Chain: "G" Number of atoms: 3355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3355 Classifications: {'peptide': 426} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 399} Chain: "L" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 793 Classifications: {'peptide': 103} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 97} Chain: "A" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 945 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "B" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 830 Classifications: {'peptide': 108} Link IDs: {'PCIS': 3, 'PTRANS': 4, 'TRANS': 100} Chain: "C" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 967 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "D" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 792 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 97} Chain: "H" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 941 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 5, 'TRANS': 113} Chain: "G" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 1.90, per 1000 atoms: 0.22 Number of scatterers: 8693 At special positions: 0 Unit cell: (81.7, 115.9, 126.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 1703 8.00 N 1441 7.00 C 5501 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS G 189 " - pdb=" SG CYS G 601 " distance=2.04 Simple disulfide: pdb=" SG CYS G 216 " - pdb=" SG CYS G 240 " distance=2.03 Simple disulfide: pdb=" SG CYS G 282 " - pdb=" SG CYS G 295 " distance=2.03 Simple disulfide: pdb=" SG CYS G 382 " - pdb=" SG CYS G 395 " distance=2.03 Simple disulfide: pdb=" SG CYS G 387 " - pdb=" SG CYS G 499 " distance=2.03 Simple disulfide: pdb=" SG CYS G 493 " - pdb=" SG CYS G 503 " distance=2.04 Simple disulfide: pdb=" SG CYS G 565 " - pdb=" SG CYS G 574 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 92 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 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 Links applied NAG-ASN " NAG G1605 " - " ASN G 417 " " NAG G1606 " - " ASN G 529 " " NAG G1607 " - " ASN G 481 " " NAG G1608 " - " ASN G 306 " " NAG G1701 " - " ASN G 378 " Time building additional restraints: 0.71 Conformation dependent library (CDL) restraints added in 297.7 milliseconds 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2032 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 22 sheets defined 4.0% alpha, 44.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'G' and resid 306 through 310 removed outlier: 3.579A pdb=" N TYR G 309 " --> pdb=" O ASN G 306 " (cutoff:3.500A) Processing helix chain 'G' and resid 393 through 398 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.798A pdb=" N PHE L 83 " --> pdb=" O THR L 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 64 removed outlier: 3.606A pdb=" N LYS A 64 " --> pdb=" O PRO A 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 61 through 64' Processing helix chain 'A' and resid 83 through 87 removed outlier: 3.761A pdb=" N THR A 87 " --> pdb=" O THR A 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 86 Processing helix chain 'D' and resid 79 through 83 removed outlier: 4.044A pdb=" N ALA D 83 " --> pdb=" O ALA D 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 4.094A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.923A pdb=" N SER H 87 " --> pdb=" O SER H 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 178 through 179 removed outlier: 6.049A pdb=" N ALA G 558 " --> pdb=" O TYR G 581 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N TYR G 581 " --> pdb=" O ALA G 558 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N LYS G 560 " --> pdb=" O GLU G 579 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU G 592 " --> pdb=" O ILE G 203 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 215 through 225 removed outlier: 6.234A pdb=" N SER G 232 " --> pdb=" O PRO G 220 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LEU G 222 " --> pdb=" O ALA G 230 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ALA G 230 " --> pdb=" O LEU G 222 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N MET G 224 " --> pdb=" O TYR G 228 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N TYR G 228 " --> pdb=" O MET G 224 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N PHE G 229 " --> pdb=" O VAL G 252 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N VAL G 252 " --> pdb=" O PHE G 229 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N TYR G 231 " --> pdb=" O ILE G 250 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ILE G 250 " --> pdb=" O TYR G 231 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N HIS G 233 " --> pdb=" O ARG G 248 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ARG G 248 " --> pdb=" O HIS G 233 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLU G 235 " --> pdb=" O LYS G 246 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N GLU G 254 " --> pdb=" O MET G 267 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N MET G 267 " --> pdb=" O GLU G 254 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU G 256 " --> pdb=" O LEU G 265 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N LEU G 265 " --> pdb=" O LEU G 256 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 279 through 287 removed outlier: 5.479A pdb=" N HIS G 281 " --> pdb=" O ALA G 296 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ALA G 296 " --> pdb=" O HIS G 281 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE G 290 " --> pdb=" O ASN G 287 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N MET G 316 " --> pdb=" O LEU G 335 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 339 through 341 removed outlier: 7.039A pdb=" N SER G 339 " --> pdb=" O VAL G 426 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N PHE G 428 " --> pdb=" O SER G 339 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N GLU G 341 " --> pdb=" O PHE G 428 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N GLU G 430 " --> pdb=" O GLU G 341 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N LYS G 425 " --> pdb=" O ASN G 417 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ASN G 417 " --> pdb=" O LYS G 425 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 339 through 341 removed outlier: 7.039A pdb=" N SER G 339 " --> pdb=" O VAL G 426 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N PHE G 428 " --> pdb=" O SER G 339 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N GLU G 341 " --> pdb=" O PHE G 428 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N GLU G 430 " --> pdb=" O GLU G 341 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N LYS G 425 " --> pdb=" O ASN G 417 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ASN G 417 " --> pdb=" O LYS G 425 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 442 through 447 removed outlier: 3.959A pdb=" N LYS G 465 " --> pdb=" O GLN G 455 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL G 476 " --> pdb=" O LEU G 470 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 512 through 515 removed outlier: 6.612A pdb=" N ILE G 520 " --> pdb=" O ILE G 514 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 4 through 7 removed outlier: 6.106A pdb=" N THR L 69 " --> pdb=" O ALA L 25 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.508A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N LYS L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LEU L 33 " --> pdb=" O LYS L 49 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 3 through 7 removed outlier: 3.574A pdb=" N THR A 25 " --> pdb=" O GLN A 3 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N THR A 21 " --> pdb=" O SER A 7 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 11 through 12 removed outlier: 4.680A pdb=" N ALA A 33 " --> pdb=" O SER A 95 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N TRP A 34 " --> pdb=" O PHE A 50 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N PHE A 50 " --> pdb=" O TRP A 34 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N TRP A 36 " --> pdb=" O MET A 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 11 through 12 removed outlier: 4.184A pdb=" N TYR A 102 " --> pdb=" O ARG A 94 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 4 through 7 Processing sheet with id=AB5, first strand: chain 'B' and resid 53 through 54 removed outlier: 6.546A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N TYR B 49 " --> pdb=" O MET B 33 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N MET B 33 " --> pdb=" O TYR B 49 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AB7, first strand: chain 'C' and resid 11 through 12 removed outlier: 6.637A pdb=" N TRP C 34 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N TYR C 50 " --> pdb=" O TRP C 34 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 11 through 12 Processing sheet with id=AB9, first strand: chain 'D' and resid 5 through 6 Processing sheet with id=AC1, first strand: chain 'D' and resid 53 through 54 removed outlier: 6.499A pdb=" N TRP D 35 " --> pdb=" O TRP D 47 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AC3, first strand: chain 'H' and resid 56 through 59 removed outlier: 6.715A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N VAL H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N ASP H 96 " --> pdb=" O PHE H 100B" (cutoff:3.500A) removed outlier: 5.378A pdb=" N PHE H 100B" --> pdb=" O ASP H 96 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 56 through 59 removed outlier: 6.715A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) 323 hydrogen bonds defined for protein. 813 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: 1.64 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1400 1.31 - 1.44: 2609 1.44 - 1.58: 4835 1.58 - 1.71: 1 1.71 - 1.84: 70 Bond restraints: 8915 Sorted by residual: bond pdb=" C SER D 14 " pdb=" N PRO D 15 " ideal model delta sigma weight residual 1.334 1.507 -0.173 1.11e-02 8.12e+03 2.43e+02 bond pdb=" C ILE D 2 " pdb=" O ILE D 2 " ideal model delta sigma weight residual 1.238 1.182 0.056 1.06e-02 8.90e+03 2.77e+01 bond pdb=" C SER A 7 " pdb=" O SER A 7 " ideal model delta sigma weight residual 1.236 1.203 0.033 7.30e-03 1.88e+04 2.05e+01 bond pdb=" C PRO D 8 " pdb=" O PRO D 8 " ideal model delta sigma weight residual 1.240 1.190 0.050 1.12e-02 7.97e+03 2.02e+01 bond pdb=" C PRO D 9 " pdb=" O PRO D 9 " ideal model delta sigma weight residual 1.237 1.183 0.054 1.32e-02 5.74e+03 1.67e+01 ... (remaining 8910 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.91: 11916 2.91 - 5.82: 175 5.82 - 8.72: 21 8.72 - 11.63: 4 11.63 - 14.54: 3 Bond angle restraints: 12119 Sorted by residual: angle pdb=" CA SER D 14 " pdb=" C SER D 14 " pdb=" N PRO D 15 " ideal model delta sigma weight residual 117.60 130.23 -12.63 1.20e+00 6.94e-01 1.11e+02 angle pdb=" C SER D 14 " pdb=" N PRO D 15 " pdb=" CA PRO D 15 " ideal model delta sigma weight residual 120.13 129.94 -9.81 1.13e+00 7.83e-01 7.54e+01 angle pdb=" O SER D 14 " pdb=" C SER D 14 " pdb=" N PRO D 15 " ideal model delta sigma weight residual 121.64 113.72 7.92 1.27e+00 6.20e-01 3.89e+01 angle pdb=" CA PRO G 392 " pdb=" N PRO G 392 " pdb=" CD PRO G 392 " ideal model delta sigma weight residual 112.00 104.72 7.28 1.40e+00 5.10e-01 2.71e+01 angle pdb=" C LYS G 569 " pdb=" N ASN G 570 " pdb=" CA ASN G 570 " ideal model delta sigma weight residual 121.54 131.29 -9.75 1.91e+00 2.74e-01 2.61e+01 ... (remaining 12114 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 4541 17.78 - 35.56: 617 35.56 - 53.35: 169 53.35 - 71.13: 27 71.13 - 88.91: 6 Dihedral angle restraints: 5360 sinusoidal: 2175 harmonic: 3185 Sorted by residual: dihedral pdb=" CA TYR H 97 " pdb=" C TYR H 97 " pdb=" N PRO H 98 " pdb=" CA PRO H 98 " ideal model delta harmonic sigma weight residual -180.00 -134.25 -45.75 0 5.00e+00 4.00e-02 8.37e+01 dihedral pdb=" C SER D 7 " pdb=" N SER D 7 " pdb=" CA SER D 7 " pdb=" CB SER D 7 " ideal model delta harmonic sigma weight residual -122.60 -138.91 16.31 0 2.50e+00 1.60e-01 4.26e+01 dihedral pdb=" N SER D 7 " pdb=" C SER D 7 " pdb=" CA SER D 7 " pdb=" CB SER D 7 " ideal model delta harmonic sigma weight residual 122.80 137.49 -14.69 0 2.50e+00 1.60e-01 3.45e+01 ... (remaining 5357 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.136: 1283 0.136 - 0.271: 36 0.271 - 0.407: 9 0.407 - 0.543: 0 0.543 - 0.679: 1 Chirality restraints: 1329 Sorted by residual: chirality pdb=" CA SER D 7 " pdb=" N SER D 7 " pdb=" C SER D 7 " pdb=" CB SER D 7 " both_signs ideal model delta sigma weight residual False 2.51 1.83 0.68 2.00e-01 2.50e+01 1.15e+01 chirality pdb=" CA ILE D 2 " pdb=" N ILE D 2 " pdb=" C ILE D 2 " pdb=" CB ILE D 2 " both_signs ideal model delta sigma weight residual False 2.43 2.79 -0.35 2.00e-01 2.50e+01 3.11e+00 chirality pdb=" CA PRO D 9 " pdb=" N PRO D 9 " pdb=" C PRO D 9 " pdb=" CB PRO D 9 " both_signs ideal model delta sigma weight residual False 2.72 2.38 0.34 2.00e-01 2.50e+01 2.90e+00 ... (remaining 1326 not shown) Planarity restraints: 1548 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR H 97 " -0.101 5.00e-02 4.00e+02 1.51e-01 3.67e+01 pdb=" N PRO H 98 " 0.262 5.00e-02 4.00e+02 pdb=" CA PRO H 98 " -0.085 5.00e-02 4.00e+02 pdb=" CD PRO H 98 " -0.076 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN G 306 " 0.035 2.00e-02 2.50e+03 3.29e-02 1.35e+01 pdb=" CG ASN G 306 " -0.035 2.00e-02 2.50e+03 pdb=" OD1 ASN G 306 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN G 306 " -0.039 2.00e-02 2.50e+03 pdb=" C1 NAG G1608 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 291 " 0.013 2.00e-02 2.50e+03 2.34e-02 1.10e+01 pdb=" CG TYR G 291 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR G 291 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR G 291 " 0.035 2.00e-02 2.50e+03 pdb=" CE1 TYR G 291 " 0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR G 291 " -0.014 2.00e-02 2.50e+03 pdb=" CZ TYR G 291 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR G 291 " -0.004 2.00e-02 2.50e+03 ... (remaining 1545 not shown) Histogram of nonbonded interaction distances: 1.36 - 2.07: 2 2.07 - 2.77: 1613 2.77 - 3.48: 11076 3.48 - 4.19: 21948 4.19 - 4.90: 38921 Nonbonded interactions: 73560 Sorted by model distance: nonbonded pdb=" OE2 GLU H 6 " pdb=" SG CYS H 92 " model vdw 1.357 3.400 nonbonded pdb=" OE2 GLU A 6 " pdb=" SG CYS A 92 " model vdw 1.539 3.400 nonbonded pdb=" OE2 GLU A 6 " pdb=" CB CYS A 92 " model vdw 2.120 3.440 nonbonded pdb=" OE2 GLU A 6 " pdb=" N CYS A 92 " model vdw 2.143 3.120 nonbonded pdb=" ND2 ASN C 35 " pdb=" OD2 ASP C 95 " model vdw 2.210 3.120 ... (remaining 73555 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: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.410 Find NCS groups from input model: 0.060 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:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.173 8933 Z= 0.327 Angle : 0.897 14.540 12160 Z= 0.506 Chirality : 0.063 0.679 1329 Planarity : 0.008 0.151 1543 Dihedral : 17.049 88.911 3289 Min Nonbonded Distance : 1.357 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.71 % Favored : 94.10 % Rotamer: Outliers : 1.03 % Allowed : 28.42 % Favored : 70.55 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 1.72 % Twisted General : 0.00 % 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: -1.10 (0.24), residues: 1085 helix: -5.13 (0.48), residues: 7 sheet: 0.05 (0.25), residues: 439 loop : -1.27 (0.22), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 68 TYR 0.049 0.002 TYR G 291 PHE 0.025 0.002 PHE C 40 TRP 0.012 0.001 TRP C 47 HIS 0.009 0.001 HIS G 233 Details of bonding type rmsd covalent geometry : bond 0.00553 ( 8915) covalent geometry : angle 0.87712 (12119) SS BOND : bond 0.00338 ( 13) SS BOND : angle 1.87374 ( 26) hydrogen bonds : bond 0.13534 ( 286) hydrogen bonds : angle 7.28701 ( 813) link_NAG-ASN : bond 0.00543 ( 5) link_NAG-ASN : angle 4.94934 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 154 time to evaluate : 0.247 Fit side-chains revert: symmetry clash REVERT: G 391 LYS cc_start: 0.7298 (mtmm) cc_final: 0.6837 (mmmt) REVERT: G 463 MET cc_start: 0.8537 (mmt) cc_final: 0.8302 (mmt) REVERT: G 531 THR cc_start: 0.8454 (m) cc_final: 0.8234 (p) REVERT: G 569 LYS cc_start: 0.7467 (mtmt) cc_final: 0.7208 (mmtt) REVERT: C 3 GLN cc_start: 0.7583 (mt0) cc_final: 0.7316 (mp10) REVERT: D 11 MET cc_start: 0.8582 (OUTLIER) cc_final: 0.7386 (tpt) REVERT: D 53 ASN cc_start: 0.8231 (m110) cc_final: 0.7896 (m110) REVERT: H 77 THR cc_start: 0.7905 (m) cc_final: 0.7661 (m) REVERT: H 107 THR cc_start: 0.7496 (t) cc_final: 0.7288 (t) outliers start: 10 outliers final: 7 residues processed: 163 average time/residue: 0.0846 time to fit residues: 19.4936 Evaluate side-chains 140 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 132 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 11 MET Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain H residue 3 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN H 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.140996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.112463 restraints weight = 10247.201| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.03 r_work: 0.3122 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 8933 Z= 0.201 Angle : 0.642 14.473 12160 Z= 0.332 Chirality : 0.047 0.280 1329 Planarity : 0.007 0.163 1543 Dihedral : 6.363 59.881 1311 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.16 % Favored : 94.75 % Rotamer: Outliers : 4.43 % Allowed : 26.88 % Favored : 68.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 1.72 % Twisted General : 0.00 % 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: -0.97 (0.24), residues: 1085 helix: -4.85 (0.68), residues: 6 sheet: 0.18 (0.25), residues: 441 loop : -1.24 (0.22), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 242 TYR 0.023 0.002 TYR G 291 PHE 0.023 0.002 PHE A 50 TRP 0.013 0.002 TRP G 519 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00474 ( 8915) covalent geometry : angle 0.63427 (12119) SS BOND : bond 0.00397 ( 13) SS BOND : angle 1.35911 ( 26) hydrogen bonds : bond 0.03802 ( 286) hydrogen bonds : angle 6.02920 ( 813) link_NAG-ASN : bond 0.00360 ( 5) link_NAG-ASN : angle 2.41010 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 134 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 291 TYR cc_start: 0.8746 (OUTLIER) cc_final: 0.8305 (t80) REVERT: G 315 MET cc_start: 0.8856 (ptm) cc_final: 0.8319 (ptm) REVERT: G 322 LYS cc_start: 0.7874 (pttt) cc_final: 0.7641 (tptm) REVERT: G 391 LYS cc_start: 0.7664 (mtmm) cc_final: 0.7226 (mmmt) REVERT: G 425 LYS cc_start: 0.7760 (tttt) cc_final: 0.7440 (ttpt) REVERT: G 446 ASP cc_start: 0.8459 (OUTLIER) cc_final: 0.8130 (t70) REVERT: G 517 ILE cc_start: 0.8378 (OUTLIER) cc_final: 0.7957 (mt) REVERT: G 530 GLN cc_start: 0.7491 (mm-40) cc_final: 0.6935 (mm-40) REVERT: G 531 THR cc_start: 0.8413 (m) cc_final: 0.8190 (p) REVERT: L 103 LYS cc_start: 0.5937 (tptp) cc_final: 0.4124 (mmmm) REVERT: A 71 ARG cc_start: 0.8437 (ptm-80) cc_final: 0.8175 (ptm-80) REVERT: B 93 GLU cc_start: 0.7748 (mt-10) cc_final: 0.7480 (mt-10) REVERT: D 71 TYR cc_start: 0.8629 (m-80) cc_final: 0.7963 (m-80) REVERT: H 31 ASN cc_start: 0.7312 (m-40) cc_final: 0.6963 (m110) REVERT: H 46 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7713 (mt-10) REVERT: H 77 THR cc_start: 0.7934 (m) cc_final: 0.7710 (m) REVERT: H 107 THR cc_start: 0.8294 (t) cc_final: 0.8075 (t) outliers start: 43 outliers final: 19 residues processed: 168 average time/residue: 0.0811 time to fit residues: 19.3333 Evaluate side-chains 148 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 126 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 188 ILE Chi-restraints excluded: chain G residue 291 TYR Chi-restraints excluded: chain G residue 311 SER Chi-restraints excluded: chain G residue 446 ASP Chi-restraints excluded: chain G residue 517 ILE Chi-restraints excluded: chain G residue 521 SER Chi-restraints excluded: chain G residue 528 SER Chi-restraints excluded: chain G residue 536 VAL Chi-restraints excluded: chain G residue 561 THR Chi-restraints excluded: chain G residue 601 CYS Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain H residue 3 LYS Chi-restraints excluded: chain H residue 93 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 65 optimal weight: 7.9990 chunk 71 optimal weight: 5.9990 chunk 1 optimal weight: 0.6980 chunk 103 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 73 optimal weight: 0.0980 chunk 56 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 287 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.135716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.107011 restraints weight = 10201.564| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.00 r_work: 0.3053 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 8933 Z= 0.228 Angle : 0.651 15.048 12160 Z= 0.333 Chirality : 0.048 0.313 1329 Planarity : 0.006 0.163 1543 Dihedral : 6.230 59.088 1304 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.25 % Favored : 94.65 % Rotamer: Outliers : 5.05 % Allowed : 26.26 % Favored : 68.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 1.72 % Twisted General : 0.00 % 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: -1.03 (0.25), residues: 1085 helix: -4.50 (1.00), residues: 6 sheet: 0.08 (0.25), residues: 450 loop : -1.25 (0.23), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 242 TYR 0.023 0.002 TYR G 291 PHE 0.024 0.002 PHE A 50 TRP 0.011 0.002 TRP A 99 HIS 0.003 0.001 HIS D 34 Details of bonding type rmsd covalent geometry : bond 0.00533 ( 8915) covalent geometry : angle 0.64356 (12119) SS BOND : bond 0.00337 ( 13) SS BOND : angle 1.40547 ( 26) hydrogen bonds : bond 0.03843 ( 286) hydrogen bonds : angle 5.91932 ( 813) link_NAG-ASN : bond 0.00350 ( 5) link_NAG-ASN : angle 2.39255 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 131 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: G 291 TYR cc_start: 0.8941 (OUTLIER) cc_final: 0.8640 (t80) REVERT: G 391 LYS cc_start: 0.7767 (mtmm) cc_final: 0.7258 (mmmt) REVERT: G 425 LYS cc_start: 0.7962 (tttt) cc_final: 0.7728 (ttpt) REVERT: G 517 ILE cc_start: 0.8483 (OUTLIER) cc_final: 0.8120 (mt) REVERT: G 530 GLN cc_start: 0.7703 (mm-40) cc_final: 0.7096 (mm-40) REVERT: G 531 THR cc_start: 0.8501 (m) cc_final: 0.8226 (p) REVERT: B 33 MET cc_start: 0.8043 (OUTLIER) cc_final: 0.7240 (tpp) REVERT: D 91 ARG cc_start: 0.8337 (mtt180) cc_final: 0.8122 (mtt180) REVERT: H 46 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7844 (mt-10) REVERT: H 77 THR cc_start: 0.8047 (m) cc_final: 0.7828 (m) outliers start: 49 outliers final: 25 residues processed: 166 average time/residue: 0.0889 time to fit residues: 20.5829 Evaluate side-chains 149 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 121 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 188 ILE Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain G residue 291 TYR Chi-restraints excluded: chain G residue 311 SER Chi-restraints excluded: chain G residue 371 VAL Chi-restraints excluded: chain G residue 517 ILE Chi-restraints excluded: chain G residue 521 SER Chi-restraints excluded: chain G residue 528 SER Chi-restraints excluded: chain G residue 536 VAL Chi-restraints excluded: chain G residue 561 THR Chi-restraints excluded: chain G residue 601 CYS Chi-restraints excluded: chain L residue 42 GLU Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 94 TRP Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain B residue 33 MET Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain H residue 3 LYS Chi-restraints excluded: chain H residue 93 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 8 optimal weight: 0.7980 chunk 71 optimal weight: 8.9990 chunk 60 optimal weight: 1.9990 chunk 74 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 chunk 90 optimal weight: 0.0040 chunk 51 optimal weight: 0.5980 chunk 58 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN C 77 GLN H 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.138241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.109491 restraints weight = 10372.843| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.04 r_work: 0.3088 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 8933 Z= 0.132 Angle : 0.574 14.561 12160 Z= 0.290 Chirality : 0.045 0.239 1329 Planarity : 0.006 0.161 1543 Dihedral : 5.966 57.020 1304 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.61 % Favored : 95.30 % Rotamer: Outliers : 5.56 % Allowed : 25.75 % Favored : 68.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 1.72 % Twisted General : 0.00 % 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: -1.00 (0.25), residues: 1085 helix: -4.20 (1.28), residues: 6 sheet: 0.00 (0.25), residues: 435 loop : -1.12 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 242 TYR 0.018 0.001 TYR G 291 PHE 0.016 0.001 PHE A 50 TRP 0.011 0.001 TRP G 519 HIS 0.003 0.001 HIS G 233 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 8915) covalent geometry : angle 0.56519 (12119) SS BOND : bond 0.00302 ( 13) SS BOND : angle 1.20055 ( 26) hydrogen bonds : bond 0.03233 ( 286) hydrogen bonds : angle 5.53115 ( 813) link_NAG-ASN : bond 0.00500 ( 5) link_NAG-ASN : angle 2.56575 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 127 time to evaluate : 0.327 Fit side-chains REVERT: G 246 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.7974 (pttt) REVERT: G 291 TYR cc_start: 0.8849 (OUTLIER) cc_final: 0.8500 (t80) REVERT: G 391 LYS cc_start: 0.7690 (mtmm) cc_final: 0.7231 (mmmt) REVERT: G 425 LYS cc_start: 0.7838 (tttt) cc_final: 0.7622 (ttpt) REVERT: G 437 SER cc_start: 0.7754 (OUTLIER) cc_final: 0.7506 (m) REVERT: G 517 ILE cc_start: 0.8487 (OUTLIER) cc_final: 0.8066 (mt) REVERT: G 530 GLN cc_start: 0.7521 (mm-40) cc_final: 0.7036 (mm-40) REVERT: G 531 THR cc_start: 0.8487 (m) cc_final: 0.8162 (p) REVERT: D 20 THR cc_start: 0.8606 (OUTLIER) cc_final: 0.8010 (m) REVERT: D 91 ARG cc_start: 0.8249 (mtt180) cc_final: 0.8043 (mtt180) REVERT: H 46 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7845 (mt-10) REVERT: H 77 THR cc_start: 0.7954 (m) cc_final: 0.7750 (m) outliers start: 54 outliers final: 32 residues processed: 169 average time/residue: 0.0720 time to fit residues: 17.2194 Evaluate side-chains 161 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 124 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 194 SER Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain G residue 246 LYS Chi-restraints excluded: chain G residue 291 TYR Chi-restraints excluded: chain G residue 311 SER Chi-restraints excluded: chain G residue 347 LYS Chi-restraints excluded: chain G residue 437 SER Chi-restraints excluded: chain G residue 440 SER Chi-restraints excluded: chain G residue 517 ILE Chi-restraints excluded: chain G residue 521 SER Chi-restraints excluded: chain G residue 536 VAL Chi-restraints excluded: chain G residue 550 GLN Chi-restraints excluded: chain G residue 561 THR Chi-restraints excluded: chain G residue 601 CYS Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 94 TRP Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain B residue 30 TYR Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 16 GLN Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain H residue 73 LYS Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 93 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 19 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.133941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.104927 restraints weight = 10373.513| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.03 r_work: 0.3025 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 8933 Z= 0.229 Angle : 0.661 14.871 12160 Z= 0.330 Chirality : 0.048 0.229 1329 Planarity : 0.006 0.162 1543 Dihedral : 6.162 59.805 1300 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.25 % Favored : 94.65 % Rotamer: Outliers : 6.80 % Allowed : 25.85 % Favored : 67.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 1.72 % Twisted General : 0.00 % 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: -1.11 (0.25), residues: 1085 helix: -3.54 (1.87), residues: 6 sheet: -0.15 (0.25), residues: 439 loop : -1.14 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG G 242 TYR 0.023 0.002 TYR G 291 PHE 0.024 0.002 PHE A 50 TRP 0.013 0.002 TRP G 519 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00540 ( 8915) covalent geometry : angle 0.63862 (12119) SS BOND : bond 0.00306 ( 13) SS BOND : angle 1.44043 ( 26) hydrogen bonds : bond 0.03647 ( 286) hydrogen bonds : angle 5.77803 ( 813) link_NAG-ASN : bond 0.00231 ( 5) link_NAG-ASN : angle 4.54459 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 129 time to evaluate : 0.321 Fit side-chains REVERT: G 291 TYR cc_start: 0.8985 (OUTLIER) cc_final: 0.8564 (t80) REVERT: G 315 MET cc_start: 0.9040 (ptm) cc_final: 0.8628 (ptm) REVERT: G 391 LYS cc_start: 0.7717 (mtmm) cc_final: 0.7204 (mmmt) REVERT: G 425 LYS cc_start: 0.8084 (tttt) cc_final: 0.7876 (ttpp) REVERT: G 437 SER cc_start: 0.7669 (OUTLIER) cc_final: 0.7395 (m) REVERT: G 446 ASP cc_start: 0.8582 (OUTLIER) cc_final: 0.8208 (t70) REVERT: G 517 ILE cc_start: 0.8502 (OUTLIER) cc_final: 0.8073 (mt) REVERT: G 529 ASN cc_start: 0.6504 (OUTLIER) cc_final: 0.5494 (t0) REVERT: A 66 ARG cc_start: 0.7481 (OUTLIER) cc_final: 0.7044 (mtp180) REVERT: A 76 ASN cc_start: 0.8001 (t0) cc_final: 0.7666 (t0) REVERT: A 102 TYR cc_start: 0.8413 (m-80) cc_final: 0.8118 (m-80) REVERT: B 93 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7754 (mt-10) REVERT: D 91 ARG cc_start: 0.8408 (mtt180) cc_final: 0.8173 (mtt180) REVERT: H 46 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7967 (mt-10) outliers start: 66 outliers final: 41 residues processed: 179 average time/residue: 0.0791 time to fit residues: 19.8342 Evaluate side-chains 173 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 126 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 188 ILE Chi-restraints excluded: chain G residue 194 SER Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain G residue 291 TYR Chi-restraints excluded: chain G residue 311 SER Chi-restraints excluded: chain G residue 347 LYS Chi-restraints excluded: chain G residue 437 SER Chi-restraints excluded: chain G residue 440 SER Chi-restraints excluded: chain G residue 446 ASP Chi-restraints excluded: chain G residue 517 ILE Chi-restraints excluded: chain G residue 521 SER Chi-restraints excluded: chain G residue 529 ASN Chi-restraints excluded: chain G residue 536 VAL Chi-restraints excluded: chain G residue 561 THR Chi-restraints excluded: chain G residue 601 CYS Chi-restraints excluded: chain L residue 42 GLU Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 94 TRP Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 30 TYR Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 16 GLN Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain H residue 73 LYS Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 108 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 62 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 94 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 chunk 90 optimal weight: 0.6980 chunk 72 optimal weight: 0.0170 chunk 78 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 75 optimal weight: 0.0170 chunk 44 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 overall best weight: 0.5056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN B 30AASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.137894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.109459 restraints weight = 10230.286| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.00 r_work: 0.3284 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 8933 Z= 0.123 Angle : 0.574 14.251 12160 Z= 0.288 Chirality : 0.044 0.168 1329 Planarity : 0.006 0.160 1543 Dihedral : 6.023 59.906 1300 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.70 % Favored : 95.21 % Rotamer: Outliers : 4.53 % Allowed : 27.81 % Favored : 67.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 1.72 % Twisted General : 0.00 % 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: -1.02 (0.25), residues: 1085 helix: -3.27 (2.16), residues: 6 sheet: -0.07 (0.25), residues: 435 loop : -1.09 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 64 TYR 0.017 0.001 TYR G 291 PHE 0.015 0.001 PHE A 50 TRP 0.012 0.001 TRP A 34 HIS 0.004 0.001 HIS L 34 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 8915) covalent geometry : angle 0.55896 (12119) SS BOND : bond 0.00281 ( 13) SS BOND : angle 1.22931 ( 26) hydrogen bonds : bond 0.03090 ( 286) hydrogen bonds : angle 5.41787 ( 813) link_NAG-ASN : bond 0.00449 ( 5) link_NAG-ASN : angle 3.41115 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 128 time to evaluate : 0.335 Fit side-chains REVERT: G 291 TYR cc_start: 0.8895 (OUTLIER) cc_final: 0.8461 (t80) REVERT: G 315 MET cc_start: 0.9042 (ptm) cc_final: 0.8601 (ptm) REVERT: G 357 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7937 (pttm) REVERT: G 517 ILE cc_start: 0.8464 (OUTLIER) cc_final: 0.8074 (mt) REVERT: G 531 THR cc_start: 0.8296 (m) cc_final: 0.7964 (p) REVERT: L 4 MET cc_start: 0.9298 (mmp) cc_final: 0.9001 (mmm) REVERT: L 103 LYS cc_start: 0.5737 (tptp) cc_final: 0.5379 (tptp) REVERT: A 76 ASN cc_start: 0.7967 (t0) cc_final: 0.7658 (t0) REVERT: A 102 TYR cc_start: 0.8262 (m-80) cc_final: 0.7904 (m-80) REVERT: B 93 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7693 (mt-10) REVERT: C 30 THR cc_start: 0.8202 (OUTLIER) cc_final: 0.7956 (p) REVERT: D 91 ARG cc_start: 0.8242 (mtt180) cc_final: 0.7998 (mtt180) outliers start: 44 outliers final: 29 residues processed: 164 average time/residue: 0.0941 time to fit residues: 21.6490 Evaluate side-chains 155 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 122 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain G residue 291 TYR Chi-restraints excluded: chain G residue 311 SER Chi-restraints excluded: chain G residue 347 LYS Chi-restraints excluded: chain G residue 357 LYS Chi-restraints excluded: chain G residue 440 SER Chi-restraints excluded: chain G residue 517 ILE Chi-restraints excluded: chain G residue 521 SER Chi-restraints excluded: chain G residue 550 GLN Chi-restraints excluded: chain G residue 561 THR Chi-restraints excluded: chain G residue 601 CYS Chi-restraints excluded: chain L residue 42 GLU Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 94 TRP Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 30 TYR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain H residue 73 LYS Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 108 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 98 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 chunk 63 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 54 optimal weight: 4.9990 chunk 78 optimal weight: 0.2980 chunk 19 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN A 1 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.137760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.109231 restraints weight = 10413.165| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.02 r_work: 0.3083 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 8933 Z= 0.135 Angle : 0.582 14.145 12160 Z= 0.290 Chirality : 0.044 0.152 1329 Planarity : 0.006 0.159 1543 Dihedral : 5.926 57.557 1300 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.35 % Favored : 94.56 % Rotamer: Outliers : 5.25 % Allowed : 27.09 % Favored : 67.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 1.72 % Twisted General : 0.00 % 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: -1.02 (0.25), residues: 1085 helix: -3.07 (2.34), residues: 6 sheet: -0.16 (0.25), residues: 445 loop : -1.03 (0.23), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 64 TYR 0.018 0.001 TYR G 291 PHE 0.016 0.001 PHE A 78 TRP 0.015 0.001 TRP G 519 HIS 0.004 0.001 HIS L 34 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 8915) covalent geometry : angle 0.55921 (12119) SS BOND : bond 0.00304 ( 13) SS BOND : angle 1.74685 ( 26) hydrogen bonds : bond 0.03090 ( 286) hydrogen bonds : angle 5.39067 ( 813) link_NAG-ASN : bond 0.00762 ( 5) link_NAG-ASN : angle 4.11465 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 128 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 291 TYR cc_start: 0.8882 (OUTLIER) cc_final: 0.8518 (t80) REVERT: G 315 MET cc_start: 0.9037 (ptm) cc_final: 0.8608 (ptm) REVERT: G 357 LYS cc_start: 0.8157 (OUTLIER) cc_final: 0.7927 (pttm) REVERT: G 517 ILE cc_start: 0.8476 (OUTLIER) cc_final: 0.7927 (mt) REVERT: G 530 GLN cc_start: 0.7530 (mm-40) cc_final: 0.6993 (mm-40) REVERT: G 531 THR cc_start: 0.8559 (OUTLIER) cc_final: 0.8211 (p) REVERT: L 4 MET cc_start: 0.9295 (mmp) cc_final: 0.8958 (mmm) REVERT: L 103 LYS cc_start: 0.5689 (tptp) cc_final: 0.5321 (tptp) REVERT: A 76 ASN cc_start: 0.8007 (t0) cc_final: 0.7647 (t0) REVERT: A 102 TYR cc_start: 0.8274 (m-80) cc_final: 0.7923 (m-80) REVERT: B 93 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7657 (mt-10) REVERT: C 30 THR cc_start: 0.8201 (OUTLIER) cc_final: 0.7960 (p) REVERT: C 110 THR cc_start: 0.8268 (OUTLIER) cc_final: 0.8048 (t) REVERT: D 11 MET cc_start: 0.7586 (ttt) cc_final: 0.7212 (ttt) REVERT: D 91 ARG cc_start: 0.8234 (mtt180) cc_final: 0.8006 (mtt180) outliers start: 51 outliers final: 38 residues processed: 164 average time/residue: 0.0816 time to fit residues: 18.6289 Evaluate side-chains 169 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 125 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain G residue 291 TYR Chi-restraints excluded: chain G residue 311 SER Chi-restraints excluded: chain G residue 347 LYS Chi-restraints excluded: chain G residue 357 LYS Chi-restraints excluded: chain G residue 437 SER Chi-restraints excluded: chain G residue 440 SER Chi-restraints excluded: chain G residue 517 ILE Chi-restraints excluded: chain G residue 521 SER Chi-restraints excluded: chain G residue 531 THR Chi-restraints excluded: chain G residue 550 GLN Chi-restraints excluded: chain G residue 561 THR Chi-restraints excluded: chain G residue 601 CYS Chi-restraints excluded: chain L residue 42 GLU Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 94 TRP Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain B residue 30 TYR Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 16 GLN Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain H residue 73 LYS Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 108 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 59 optimal weight: 4.9990 chunk 86 optimal weight: 0.0970 chunk 71 optimal weight: 7.9990 chunk 79 optimal weight: 0.4980 chunk 21 optimal weight: 0.4980 chunk 52 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 chunk 62 optimal weight: 0.0980 chunk 85 optimal weight: 0.4980 overall best weight: 0.3378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.140394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.112209 restraints weight = 10155.470| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.00 r_work: 0.3122 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.074 8933 Z= 0.103 Angle : 0.553 13.848 12160 Z= 0.275 Chirality : 0.044 0.193 1329 Planarity : 0.006 0.158 1543 Dihedral : 5.389 53.819 1300 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.70 % Favored : 95.21 % Rotamer: Outliers : 4.53 % Allowed : 27.39 % Favored : 68.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 1.72 % Twisted General : 0.00 % 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: -0.83 (0.25), residues: 1085 helix: -3.03 (2.39), residues: 6 sheet: 0.11 (0.26), residues: 425 loop : -0.98 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 64 TYR 0.017 0.001 TYR G 291 PHE 0.013 0.001 PHE A 78 TRP 0.012 0.001 TRP G 519 HIS 0.004 0.001 HIS L 34 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 8915) covalent geometry : angle 0.53227 (12119) SS BOND : bond 0.00269 ( 13) SS BOND : angle 1.20780 ( 26) hydrogen bonds : bond 0.02891 ( 286) hydrogen bonds : angle 5.13689 ( 813) link_NAG-ASN : bond 0.00521 ( 5) link_NAG-ASN : angle 4.11219 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 135 time to evaluate : 0.336 Fit side-chains revert: symmetry clash REVERT: G 246 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.8028 (pttt) REVERT: G 291 TYR cc_start: 0.8834 (OUTLIER) cc_final: 0.8436 (t80) REVERT: G 315 MET cc_start: 0.9019 (ptm) cc_final: 0.8731 (ptm) REVERT: G 357 LYS cc_start: 0.8120 (OUTLIER) cc_final: 0.7891 (pttm) REVERT: G 530 GLN cc_start: 0.7394 (mm-40) cc_final: 0.6812 (mm-40) REVERT: G 531 THR cc_start: 0.8537 (OUTLIER) cc_final: 0.8219 (p) REVERT: L 103 LYS cc_start: 0.5402 (tptp) cc_final: 0.3821 (mtpt) REVERT: A 76 ASN cc_start: 0.7968 (t0) cc_final: 0.7644 (t0) REVERT: A 102 TYR cc_start: 0.8228 (m-80) cc_final: 0.7880 (m-80) REVERT: B 93 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7728 (mt-10) REVERT: D 61 ARG cc_start: 0.8123 (ptp90) cc_final: 0.7639 (ptp90) REVERT: H 31 ASN cc_start: 0.7132 (m110) cc_final: 0.6910 (m-40) outliers start: 44 outliers final: 33 residues processed: 170 average time/residue: 0.0828 time to fit residues: 20.0608 Evaluate side-chains 168 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 131 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 188 ILE Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain G residue 218 THR Chi-restraints excluded: chain G residue 246 LYS Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain G residue 291 TYR Chi-restraints excluded: chain G residue 311 SER Chi-restraints excluded: chain G residue 347 LYS Chi-restraints excluded: chain G residue 357 LYS Chi-restraints excluded: chain G residue 440 SER Chi-restraints excluded: chain G residue 521 SER Chi-restraints excluded: chain G residue 531 THR Chi-restraints excluded: chain G residue 550 GLN Chi-restraints excluded: chain G residue 561 THR Chi-restraints excluded: chain G residue 601 CYS Chi-restraints excluded: chain L residue 42 GLU Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain B residue 30 TYR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 73 LYS Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 108 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 96 optimal weight: 6.9990 chunk 58 optimal weight: 0.5980 chunk 85 optimal weight: 0.0870 chunk 103 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 26 optimal weight: 0.0020 chunk 66 optimal weight: 4.9990 chunk 92 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 overall best weight: 0.4568 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 559 GLN ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.139981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.111841 restraints weight = 10251.252| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.98 r_work: 0.3317 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 8933 Z= 0.114 Angle : 0.553 13.751 12160 Z= 0.276 Chirality : 0.044 0.206 1329 Planarity : 0.006 0.158 1543 Dihedral : 5.259 49.161 1300 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.44 % Favored : 94.47 % Rotamer: Outliers : 4.63 % Allowed : 27.29 % Favored : 68.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 1.72 % Twisted General : 0.00 % 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: -0.77 (0.25), residues: 1085 helix: -3.08 (2.33), residues: 6 sheet: 0.18 (0.26), residues: 419 loop : -0.96 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 91 TYR 0.018 0.001 TYR G 291 PHE 0.015 0.001 PHE A 78 TRP 0.011 0.001 TRP G 519 HIS 0.004 0.001 HIS L 34 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 8915) covalent geometry : angle 0.53259 (12119) SS BOND : bond 0.00261 ( 13) SS BOND : angle 1.16490 ( 26) hydrogen bonds : bond 0.02955 ( 286) hydrogen bonds : angle 5.12661 ( 813) link_NAG-ASN : bond 0.00642 ( 5) link_NAG-ASN : angle 4.07493 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 132 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: G 246 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.8116 (pttt) REVERT: G 291 TYR cc_start: 0.8894 (OUTLIER) cc_final: 0.8473 (t80) REVERT: G 315 MET cc_start: 0.9010 (ptm) cc_final: 0.8552 (ptm) REVERT: G 357 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7891 (pttm) REVERT: G 530 GLN cc_start: 0.7499 (mm-40) cc_final: 0.6964 (mm-40) REVERT: G 531 THR cc_start: 0.8525 (OUTLIER) cc_final: 0.8242 (p) REVERT: L 4 MET cc_start: 0.9309 (mmp) cc_final: 0.8941 (mmm) REVERT: L 103 LYS cc_start: 0.5405 (tptp) cc_final: 0.3812 (mtpt) REVERT: A 71 ARG cc_start: 0.8719 (ptm-80) cc_final: 0.8465 (ptm-80) REVERT: A 76 ASN cc_start: 0.7952 (t0) cc_final: 0.7566 (t0) REVERT: A 102 TYR cc_start: 0.8210 (m-80) cc_final: 0.7878 (m-80) REVERT: B 93 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7761 (mt-10) REVERT: C 110 THR cc_start: 0.8200 (OUTLIER) cc_final: 0.7981 (t) REVERT: D 61 ARG cc_start: 0.8153 (ptp90) cc_final: 0.7634 (ptp90) REVERT: H 31 ASN cc_start: 0.7203 (m110) cc_final: 0.6948 (m-40) REVERT: H 64 ARG cc_start: 0.6599 (ttm-80) cc_final: 0.6397 (ttm-80) outliers start: 45 outliers final: 36 residues processed: 165 average time/residue: 0.0811 time to fit residues: 19.1671 Evaluate side-chains 173 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 132 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain G residue 218 THR Chi-restraints excluded: chain G residue 246 LYS Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain G residue 291 TYR Chi-restraints excluded: chain G residue 311 SER Chi-restraints excluded: chain G residue 347 LYS Chi-restraints excluded: chain G residue 357 LYS Chi-restraints excluded: chain G residue 437 SER Chi-restraints excluded: chain G residue 440 SER Chi-restraints excluded: chain G residue 521 SER Chi-restraints excluded: chain G residue 531 THR Chi-restraints excluded: chain G residue 536 VAL Chi-restraints excluded: chain G residue 550 GLN Chi-restraints excluded: chain G residue 561 THR Chi-restraints excluded: chain G residue 601 CYS Chi-restraints excluded: chain L residue 42 GLU Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain B residue 30 TYR Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 73 LYS Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 108 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 105 optimal weight: 0.7980 chunk 60 optimal weight: 5.9990 chunk 4 optimal weight: 0.5980 chunk 98 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 70 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 50 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30AASN ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.135031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.106234 restraints weight = 10334.862| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.00 r_work: 0.3243 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 8933 Z= 0.199 Angle : 0.621 13.965 12160 Z= 0.312 Chirality : 0.047 0.252 1329 Planarity : 0.006 0.159 1543 Dihedral : 5.470 45.833 1300 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.71 % Favored : 94.19 % Rotamer: Outliers : 4.94 % Allowed : 26.78 % Favored : 68.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 1.72 % Twisted General : 0.00 % 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: -0.97 (0.25), residues: 1085 helix: -2.93 (2.42), residues: 6 sheet: -0.21 (0.25), residues: 447 loop : -0.92 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 61 TYR 0.022 0.002 TYR G 291 PHE 0.020 0.002 PHE A 50 TRP 0.009 0.001 TRP G 573 HIS 0.005 0.001 HIS L 34 Details of bonding type rmsd covalent geometry : bond 0.00473 ( 8915) covalent geometry : angle 0.59972 (12119) SS BOND : bond 0.00324 ( 13) SS BOND : angle 1.41979 ( 26) hydrogen bonds : bond 0.03419 ( 286) hydrogen bonds : angle 5.54331 ( 813) link_NAG-ASN : bond 0.00594 ( 5) link_NAG-ASN : angle 4.35229 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 115 time to evaluate : 0.252 Fit side-chains revert: symmetry clash REVERT: G 246 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8092 (pttt) REVERT: G 291 TYR cc_start: 0.8995 (OUTLIER) cc_final: 0.8603 (t80) REVERT: G 315 MET cc_start: 0.9086 (ptm) cc_final: 0.8635 (ptm) REVERT: G 530 GLN cc_start: 0.7607 (mm-40) cc_final: 0.7026 (mm-40) REVERT: G 531 THR cc_start: 0.8527 (OUTLIER) cc_final: 0.8198 (p) REVERT: L 103 LYS cc_start: 0.5383 (tptp) cc_final: 0.5008 (tptp) REVERT: A 76 ASN cc_start: 0.8019 (t0) cc_final: 0.7462 (t0) REVERT: A 102 TYR cc_start: 0.8327 (m-80) cc_final: 0.7932 (m-80) REVERT: B 93 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7675 (mt-10) REVERT: H 64 ARG cc_start: 0.6632 (ttm-80) cc_final: 0.6406 (ttm-80) REVERT: H 82 ASN cc_start: 0.7085 (OUTLIER) cc_final: 0.6763 (p0) outliers start: 48 outliers final: 39 residues processed: 150 average time/residue: 0.0695 time to fit residues: 14.9338 Evaluate side-chains 157 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 114 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 188 ILE Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain G residue 218 THR Chi-restraints excluded: chain G residue 246 LYS Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain G residue 291 TYR Chi-restraints excluded: chain G residue 311 SER Chi-restraints excluded: chain G residue 347 LYS Chi-restraints excluded: chain G residue 437 SER Chi-restraints excluded: chain G residue 440 SER Chi-restraints excluded: chain G residue 483 THR Chi-restraints excluded: chain G residue 521 SER Chi-restraints excluded: chain G residue 531 THR Chi-restraints excluded: chain G residue 536 VAL Chi-restraints excluded: chain G residue 561 THR Chi-restraints excluded: chain G residue 601 CYS Chi-restraints excluded: chain L residue 42 GLU Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 30 TYR Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 16 GLN Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain H residue 73 LYS Chi-restraints excluded: chain H residue 82 ASN Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 108 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 77 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 103 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 26 optimal weight: 0.0980 chunk 88 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.135251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.106552 restraints weight = 10318.591| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 1.99 r_work: 0.3048 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.225 8933 Z= 0.275 Angle : 0.932 59.194 12160 Z= 0.542 Chirality : 0.052 0.868 1329 Planarity : 0.006 0.159 1543 Dihedral : 5.476 45.830 1300 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.71 % Favored : 94.19 % Rotamer: Outliers : 4.53 % Allowed : 27.60 % Favored : 67.87 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 1.72 % Twisted General : 0.00 % 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: -0.98 (0.25), residues: 1085 helix: -2.92 (2.43), residues: 6 sheet: -0.21 (0.25), residues: 447 loop : -0.92 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 91 TYR 0.021 0.002 TYR G 291 PHE 0.020 0.002 PHE A 50 TRP 0.010 0.001 TRP G 519 HIS 0.004 0.001 HIS L 34 Details of bonding type rmsd covalent geometry : bond 0.00549 ( 8915) covalent geometry : angle 0.91921 (12119) SS BOND : bond 0.00354 ( 13) SS BOND : angle 1.38342 ( 26) hydrogen bonds : bond 0.03423 ( 286) hydrogen bonds : angle 5.54195 ( 813) link_NAG-ASN : bond 0.00583 ( 5) link_NAG-ASN : angle 4.34838 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2260.37 seconds wall clock time: 39 minutes 26.32 seconds (2366.32 seconds total)