Starting phenix.real_space_refine on Sat Aug 23 11:30:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o5w_70149/08_2025/9o5w_70149.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o5w_70149/08_2025/9o5w_70149.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9o5w_70149/08_2025/9o5w_70149.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o5w_70149/08_2025/9o5w_70149.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9o5w_70149/08_2025/9o5w_70149.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o5w_70149/08_2025/9o5w_70149.map" } resolution = 2.67 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= 0.001 sd= 0.059 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 93 5.16 5 C 7107 2.51 5 N 1977 2.21 5 O 2244 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11421 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2530 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 22, 'TRANS': 313} Chain: "C" Number of atoms: 2530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2530 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 22, 'TRANS': 313} Chain: "E" Number of atoms: 2530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2530 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 22, 'TRANS': 313} Chain: "B" Number of atoms: 1221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1221 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 3, 'TRANS': 154} Chain: "D" Number of atoms: 1221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1221 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 3, 'TRANS': 154} Chain: "F" Number of atoms: 1221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1221 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 3, 'TRANS': 154} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.20, per 1000 atoms: 0.19 Number of scatterers: 11421 At special positions: 0 Unit cell: (88.825, 87.78, 137.94, 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 93 16.00 O 2244 8.00 N 1977 7.00 C 7107 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 9 " - pdb=" SG CYS B 484 " distance=2.03 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 77 " distance=2.03 Simple disulfide: pdb=" SG CYS A 99 " - pdb=" SG CYS A 148 " distance=2.03 Simple disulfide: pdb=" SG CYS A 183 " - pdb=" SG CYS A 277 " distance=2.04 Simple disulfide: pdb=" SG CYS A 298 " - pdb=" SG CYS A 324 " distance=2.02 Simple disulfide: pdb=" SG CYS C 9 " - pdb=" SG CYS D 484 " distance=2.03 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 77 " distance=2.03 Simple disulfide: pdb=" SG CYS C 99 " - pdb=" SG CYS C 148 " distance=2.03 Simple disulfide: pdb=" SG CYS C 183 " - pdb=" SG CYS C 277 " distance=2.04 Simple disulfide: pdb=" SG CYS C 298 " - pdb=" SG CYS C 324 " distance=2.02 Simple disulfide: pdb=" SG CYS E 9 " - pdb=" SG CYS F 484 " distance=2.03 Simple disulfide: pdb=" SG CYS E 65 " - pdb=" SG CYS E 77 " distance=2.03 Simple disulfide: pdb=" SG CYS E 99 " - pdb=" SG CYS E 148 " distance=2.03 Simple disulfide: pdb=" SG CYS E 183 " - pdb=" SG CYS E 277 " distance=2.04 Simple disulfide: pdb=" SG CYS E 298 " - pdb=" SG CYS E 324 " distance=2.02 Simple disulfide: pdb=" SG CYS B 491 " - pdb=" SG CYS B 495 " distance=2.02 Simple disulfide: pdb=" SG CYS D 491 " - pdb=" SG CYS D 495 " distance=2.03 Simple disulfide: pdb=" SG CYS F 491 " - pdb=" SG CYS F 495 " distance=2.02 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 BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG O 1 " - " NAG O 2 " " NAG Q 1 " - " NAG Q 2 " NAG-ASN " NAG G 1 " - " ASN A 36 " " NAG I 1 " - " ASN A 336 " " NAG K 1 " - " ASN C 36 " " NAG M 1 " - " ASN C 336 " " NAG O 1 " - " ASN E 36 " " NAG Q 1 " - " ASN E 336 " Time building additional restraints: 0.99 Conformation dependent library (CDL) restraints added in 403.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2688 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 30 sheets defined 25.3% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 66 through 72 Processing helix chain 'A' and resid 103 through 107 removed outlier: 3.836A pdb=" N GLY A 107 " --> pdb=" O HIS A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 117 Processing helix chain 'A' and resid 131 through 135 Processing helix chain 'A' and resid 199 through 208 Processing helix chain 'C' and resid 66 through 72 Processing helix chain 'C' and resid 103 through 107 removed outlier: 3.863A pdb=" N GLY C 107 " --> pdb=" O HIS C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 117 removed outlier: 3.505A pdb=" N ARG C 117 " --> pdb=" O PRO C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 135 Processing helix chain 'C' and resid 199 through 208 Processing helix chain 'E' and resid 66 through 72 Processing helix chain 'E' and resid 103 through 107 removed outlier: 3.845A pdb=" N GLY E 107 " --> pdb=" O HIS E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 117 removed outlier: 3.528A pdb=" N ARG E 117 " --> pdb=" O PRO E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 135 Processing helix chain 'E' and resid 199 through 208 Processing helix chain 'B' and resid 384 through 401 Processing helix chain 'B' and resid 402 through 407 removed outlier: 3.982A pdb=" N THR B 406 " --> pdb=" O ASN B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 473 removed outlier: 3.567A pdb=" N GLU B 458 " --> pdb=" O ILE B 454 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ASP B 459 " --> pdb=" O ILE B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 501 Processing helix chain 'B' and resid 505 through 510 Processing helix chain 'D' and resid 384 through 401 Processing helix chain 'D' and resid 402 through 407 removed outlier: 3.988A pdb=" N THR D 406 " --> pdb=" O ASN D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 473 removed outlier: 3.597A pdb=" N GLU D 458 " --> pdb=" O ILE D 454 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ASP D 459 " --> pdb=" O ILE D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 493 through 501 Processing helix chain 'D' and resid 505 through 510 Processing helix chain 'F' and resid 384 through 401 Processing helix chain 'F' and resid 402 through 407 removed outlier: 3.962A pdb=" N THR F 406 " --> pdb=" O ASN F 403 " (cutoff:3.500A) Processing helix chain 'F' and resid 421 through 473 removed outlier: 3.509A pdb=" N GLU F 458 " --> pdb=" O ILE F 454 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASP F 459 " --> pdb=" O ILE F 455 " (cutoff:3.500A) Processing helix chain 'F' and resid 493 through 501 Processing helix chain 'F' and resid 505 through 510 Processing sheet with id=AA1, first strand: chain 'B' and resid 378 through 383 removed outlier: 3.608A pdb=" N LYS A 7 " --> pdb=" O THR B 374 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 22 Processing sheet with id=AA3, first strand: chain 'A' and resid 34 through 36 Processing sheet with id=AA4, first strand: chain 'A' and resid 38 through 39 Processing sheet with id=AA5, first strand: chain 'A' and resid 87 through 89 Processing sheet with id=AA6, first strand: chain 'A' and resid 122 through 125 removed outlier: 4.188A pdb=" N PHE A 275 " --> pdb=" O SER A 125 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N VAL A 192 " --> pdb=" O PRO A 272 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N PHE A 269 " --> pdb=" O LEU A 164 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LEU A 164 " --> pdb=" O PHE A 269 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 122 through 125 removed outlier: 4.188A pdb=" N PHE A 275 " --> pdb=" O SER A 125 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 149 through 150 removed outlier: 4.216A pdb=" N VAL A 154 " --> pdb=" O ASP A 150 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 175 through 180 Processing sheet with id=AB1, first strand: chain 'A' and resid 305 through 306 Processing sheet with id=AB2, first strand: chain 'D' and resid 378 through 383 removed outlier: 3.593A pdb=" N LYS C 7 " --> pdb=" O THR D 374 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 19 through 22 Processing sheet with id=AB4, first strand: chain 'C' and resid 34 through 36 Processing sheet with id=AB5, first strand: chain 'C' and resid 38 through 39 Processing sheet with id=AB6, first strand: chain 'C' and resid 87 through 89 Processing sheet with id=AB7, first strand: chain 'C' and resid 122 through 125 removed outlier: 4.232A pdb=" N PHE C 275 " --> pdb=" O SER C 125 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N VAL C 192 " --> pdb=" O PRO C 272 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N PHE C 269 " --> pdb=" O LEU C 164 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEU C 164 " --> pdb=" O PHE C 269 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 122 through 125 removed outlier: 4.232A pdb=" N PHE C 275 " --> pdb=" O SER C 125 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 149 through 150 removed outlier: 4.235A pdb=" N VAL C 154 " --> pdb=" O ASP C 150 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 175 through 180 Processing sheet with id=AC2, first strand: chain 'C' and resid 305 through 306 Processing sheet with id=AC3, first strand: chain 'F' and resid 378 through 383 removed outlier: 3.579A pdb=" N LYS E 7 " --> pdb=" O THR F 374 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 19 through 22 Processing sheet with id=AC5, first strand: chain 'E' and resid 34 through 36 Processing sheet with id=AC6, first strand: chain 'E' and resid 38 through 39 Processing sheet with id=AC7, first strand: chain 'E' and resid 87 through 89 Processing sheet with id=AC8, first strand: chain 'E' and resid 122 through 125 removed outlier: 4.193A pdb=" N PHE E 275 " --> pdb=" O SER E 125 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N VAL E 192 " --> pdb=" O PRO E 272 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N PHE E 269 " --> pdb=" O LEU E 164 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU E 164 " --> pdb=" O PHE E 269 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 122 through 125 removed outlier: 4.193A pdb=" N PHE E 275 " --> pdb=" O SER E 125 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 149 through 150 removed outlier: 4.199A pdb=" N VAL E 154 " --> pdb=" O ASP E 150 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 175 through 180 Processing sheet with id=AD3, first strand: chain 'E' and resid 305 through 306 481 hydrogen bonds defined for protein. 1272 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: 1.65 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3788 1.34 - 1.47: 2553 1.47 - 1.59: 5146 1.59 - 1.71: 0 1.71 - 1.83: 144 Bond restraints: 11631 Sorted by residual: bond pdb=" C1 NAG K 2 " pdb=" O5 NAG K 2 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.71e+00 bond pdb=" C1 NAG O 2 " pdb=" O5 NAG O 2 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.45e+00 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.32e+00 bond pdb=" C1 NAG M 2 " pdb=" O5 NAG M 2 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.31e+00 bond pdb=" C1 NAG Q 2 " pdb=" O5 NAG Q 2 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.28e+00 ... (remaining 11626 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 14653 2.15 - 4.31: 937 4.31 - 6.46: 118 6.46 - 8.61: 37 8.61 - 10.77: 11 Bond angle restraints: 15756 Sorted by residual: angle pdb=" N ILE D 365 " pdb=" CA ILE D 365 " pdb=" C ILE D 365 " ideal model delta sigma weight residual 110.72 104.66 6.06 1.01e+00 9.80e-01 3.60e+01 angle pdb=" N ILE F 365 " pdb=" CA ILE F 365 " pdb=" C ILE F 365 " ideal model delta sigma weight residual 110.72 104.72 6.00 1.01e+00 9.80e-01 3.53e+01 angle pdb=" C ILE D 365 " pdb=" N ALA D 366 " pdb=" CA ALA D 366 " ideal model delta sigma weight residual 121.54 131.71 -10.17 1.91e+00 2.74e-01 2.84e+01 angle pdb=" C ILE F 365 " pdb=" N ALA F 366 " pdb=" CA ALA F 366 " ideal model delta sigma weight residual 121.54 131.62 -10.08 1.91e+00 2.74e-01 2.78e+01 angle pdb=" N ILE B 365 " pdb=" CA ILE B 365 " pdb=" C ILE B 365 " ideal model delta sigma weight residual 110.72 105.40 5.32 1.01e+00 9.80e-01 2.78e+01 ... (remaining 15751 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 6770 17.81 - 35.61: 302 35.61 - 53.42: 114 53.42 - 71.23: 44 71.23 - 89.03: 15 Dihedral angle restraints: 7245 sinusoidal: 3048 harmonic: 4197 Sorted by residual: dihedral pdb=" CB CYS A 99 " pdb=" SG CYS A 99 " pdb=" SG CYS A 148 " pdb=" CB CYS A 148 " ideal model delta sinusoidal sigma weight residual 93.00 142.34 -49.34 1 1.00e+01 1.00e-02 3.35e+01 dihedral pdb=" CB CYS E 99 " pdb=" SG CYS E 99 " pdb=" SG CYS E 148 " pdb=" CB CYS E 148 " ideal model delta sinusoidal sigma weight residual 93.00 141.93 -48.93 1 1.00e+01 1.00e-02 3.29e+01 dihedral pdb=" CB CYS C 99 " pdb=" SG CYS C 99 " pdb=" SG CYS C 148 " pdb=" CB CYS C 148 " ideal model delta sinusoidal sigma weight residual 93.00 141.53 -48.53 1 1.00e+01 1.00e-02 3.24e+01 ... (remaining 7242 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1304 0.060 - 0.120: 435 0.120 - 0.180: 72 0.180 - 0.240: 11 0.240 - 0.299: 2 Chirality restraints: 1824 Sorted by residual: chirality pdb=" C1 NAG Q 1 " pdb=" ND2 ASN E 336 " pdb=" C2 NAG Q 1 " pdb=" O5 NAG Q 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" CA MET F 364 " pdb=" N MET F 364 " pdb=" C MET F 364 " pdb=" CB MET F 364 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CA MET D 364 " pdb=" N MET D 364 " pdb=" C MET D 364 " pdb=" CB MET D 364 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 1821 not shown) Planarity restraints: 2040 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP E 137 " -0.013 2.00e-02 2.50e+03 2.69e-02 7.22e+00 pdb=" C ASP E 137 " 0.046 2.00e-02 2.50e+03 pdb=" O ASP E 137 " -0.018 2.00e-02 2.50e+03 pdb=" N GLN E 138 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 222 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.82e+00 pdb=" C GLY C 222 " 0.045 2.00e-02 2.50e+03 pdb=" O GLY C 222 " -0.017 2.00e-02 2.50e+03 pdb=" N ARG C 223 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY E 222 " 0.013 2.00e-02 2.50e+03 2.58e-02 6.63e+00 pdb=" C GLY E 222 " -0.045 2.00e-02 2.50e+03 pdb=" O GLY E 222 " 0.017 2.00e-02 2.50e+03 pdb=" N ARG E 223 " 0.015 2.00e-02 2.50e+03 ... (remaining 2037 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 130 2.62 - 3.19: 9381 3.19 - 3.76: 17727 3.76 - 4.33: 25685 4.33 - 4.90: 42123 Nonbonded interactions: 95046 Sorted by model distance: nonbonded pdb=" OD1 ASN C 100 " pdb=" OG SER C 145 " model vdw 2.048 3.040 nonbonded pdb=" OD1 ASN E 100 " pdb=" OG SER E 145 " model vdw 2.053 3.040 nonbonded pdb=" OD1 ASN A 100 " pdb=" OG SER A 145 " model vdw 2.075 3.040 nonbonded pdb=" OG1 THR D 406 " pdb=" OE2 GLU D 407 " model vdw 2.100 3.040 nonbonded pdb=" O SER C 125 " pdb=" OG SER C 125 " model vdw 2.356 3.040 ... (remaining 95041 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.670 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: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 10.080 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 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:7.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 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 : 0.007 0.059 11661 Z= 0.281 Angle : 1.215 10.765 15828 Z= 0.678 Chirality : 0.059 0.299 1824 Planarity : 0.006 0.046 2034 Dihedral : 13.570 89.035 4503 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 1.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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 aren not related in a simple way. whole: 0.41 (0.20), residues: 1470 helix: 0.48 (0.26), residues: 318 sheet: 0.46 (0.31), residues: 270 loop : 0.25 (0.19), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 329 TYR 0.017 0.003 TYR E 265 PHE 0.026 0.003 PHE C 158 TRP 0.015 0.002 TRP E 327 HIS 0.015 0.003 HIS A 181 Details of bonding type rmsd covalent geometry : bond 0.00657 (11631) covalent geometry : angle 1.20405 (15756) SS BOND : bond 0.00631 ( 18) SS BOND : angle 2.76994 ( 36) hydrogen bonds : bond 0.15973 ( 460) hydrogen bonds : angle 6.54744 ( 1272) link_BETA1-4 : bond 0.00180 ( 6) link_BETA1-4 : angle 2.66993 ( 18) link_NAG-ASN : bond 0.00460 ( 6) link_NAG-ASN : angle 2.49121 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.497 Fit side-chains REVERT: A 16 LYS cc_start: 0.8096 (tttp) cc_final: 0.7815 (pptt) REVERT: A 98 LYS cc_start: 0.8159 (mmtm) cc_final: 0.7896 (mmmt) REVERT: A 339 LYS cc_start: 0.8082 (ptpt) cc_final: 0.7553 (pttt) REVERT: C 16 LYS cc_start: 0.8192 (tttp) cc_final: 0.7901 (ptmt) REVERT: C 68 MET cc_start: 0.9234 (tpp) cc_final: 0.8944 (tpp) REVERT: C 339 LYS cc_start: 0.8170 (mtmm) cc_final: 0.7832 (mtpm) REVERT: B 390 LYS cc_start: 0.7538 (tttm) cc_final: 0.7329 (ttmp) REVERT: D 472 MET cc_start: 0.8274 (mtm) cc_final: 0.8068 (ttm) REVERT: D 498 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7374 (mt-10) REVERT: F 435 ARG cc_start: 0.8432 (ttt180) cc_final: 0.8020 (ttt180) REVERT: F 438 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7637 (mm-30) REVERT: F 450 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7714 (mm-30) REVERT: F 459 ASP cc_start: 0.7847 (m-30) cc_final: 0.7628 (m-30) REVERT: F 480 MET cc_start: 0.8492 (mtm) cc_final: 0.8066 (mtm) REVERT: F 507 SER cc_start: 0.8657 (p) cc_final: 0.8330 (p) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.7293 time to fit residues: 150.1051 Evaluate side-chains 135 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 GLN A 292 ASN C 182 GLN E 167 ASN B 403 ASN B 442 GLN B 490 GLN D 400 ASN D 403 ASN F 400 ASN F 490 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.125029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.104746 restraints weight = 14353.583| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.62 r_work: 0.3204 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11661 Z= 0.154 Angle : 0.650 8.916 15828 Z= 0.344 Chirality : 0.045 0.198 1824 Planarity : 0.005 0.039 2034 Dihedral : 5.582 37.910 1818 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.42 % Allowed : 10.23 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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 aren not related in a simple way. whole: 0.67 (0.21), residues: 1470 helix: 1.83 (0.28), residues: 324 sheet: 0.20 (0.27), residues: 336 loop : 0.07 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 497 TYR 0.008 0.002 TYR F 509 PHE 0.018 0.002 PHE C 275 TRP 0.007 0.001 TRP B 368 HIS 0.008 0.001 HIS B 461 Details of bonding type rmsd covalent geometry : bond 0.00343 (11631) covalent geometry : angle 0.64239 (15756) SS BOND : bond 0.00315 ( 18) SS BOND : angle 1.53263 ( 36) hydrogen bonds : bond 0.05495 ( 460) hydrogen bonds : angle 5.36017 ( 1272) link_BETA1-4 : bond 0.00385 ( 6) link_BETA1-4 : angle 1.48079 ( 18) link_NAG-ASN : bond 0.00419 ( 6) link_NAG-ASN : angle 1.75392 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 154 time to evaluate : 0.457 Fit side-chains REVERT: A 92 ASN cc_start: 0.8101 (m-40) cc_final: 0.7453 (p0) REVERT: C 48 ASP cc_start: 0.8323 (m-30) cc_final: 0.8073 (m-30) REVERT: C 68 MET cc_start: 0.9253 (tpp) cc_final: 0.8963 (tpp) REVERT: E 339 LYS cc_start: 0.8161 (tttp) cc_final: 0.7723 (mtmt) REVERT: B 412 VAL cc_start: 0.7203 (OUTLIER) cc_final: 0.6920 (p) REVERT: D 364 MET cc_start: 0.2165 (mtt) cc_final: 0.1955 (mtt) REVERT: D 385 LEU cc_start: 0.8374 (mm) cc_final: 0.8144 (mt) REVERT: D 498 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7485 (mt-10) REVERT: F 435 ARG cc_start: 0.8635 (ttt180) cc_final: 0.8294 (ttt180) REVERT: F 438 GLU cc_start: 0.8410 (mm-30) cc_final: 0.8115 (mm-30) REVERT: F 480 MET cc_start: 0.8714 (mtm) cc_final: 0.8422 (mtp) REVERT: F 512 ASP cc_start: 0.8085 (m-30) cc_final: 0.7651 (m-30) outliers start: 30 outliers final: 9 residues processed: 167 average time/residue: 0.5899 time to fit residues: 105.6059 Evaluate side-chains 141 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 131 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 ASP Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 495 CYS Chi-restraints excluded: chain F residue 374 THR Chi-restraints excluded: chain F residue 412 VAL Chi-restraints excluded: chain F residue 495 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 76 optimal weight: 0.5980 chunk 75 optimal weight: 0.8980 chunk 117 optimal weight: 0.9980 chunk 125 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 chunk 110 optimal weight: 4.9990 chunk 142 optimal weight: 6.9990 chunk 127 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 167 ASN B 369 HIS B 403 ASN B 442 GLN B 461 HIS D 403 ASN F 442 GLN F 490 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.123526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.102995 restraints weight = 14446.225| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.62 r_work: 0.3174 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11661 Z= 0.141 Angle : 0.592 8.215 15828 Z= 0.308 Chirality : 0.044 0.172 1824 Planarity : 0.004 0.043 2034 Dihedral : 5.273 35.810 1818 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.90 % Allowed : 11.19 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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 aren not related in a simple way. whole: 0.72 (0.21), residues: 1470 helix: 2.17 (0.28), residues: 321 sheet: 0.16 (0.28), residues: 336 loop : -0.01 (0.21), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 497 TYR 0.007 0.001 TYR F 509 PHE 0.017 0.002 PHE C 275 TRP 0.005 0.001 TRP A 327 HIS 0.005 0.001 HIS B 461 Details of bonding type rmsd covalent geometry : bond 0.00317 (11631) covalent geometry : angle 0.58413 (15756) SS BOND : bond 0.00252 ( 18) SS BOND : angle 1.26400 ( 36) hydrogen bonds : bond 0.04934 ( 460) hydrogen bonds : angle 5.12530 ( 1272) link_BETA1-4 : bond 0.00346 ( 6) link_BETA1-4 : angle 1.67168 ( 18) link_NAG-ASN : bond 0.00284 ( 6) link_NAG-ASN : angle 1.76774 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 158 time to evaluate : 0.474 Fit side-chains REVERT: A 92 ASN cc_start: 0.8117 (m-40) cc_final: 0.7558 (p0) REVERT: C 68 MET cc_start: 0.9231 (tpp) cc_final: 0.8949 (tpp) REVERT: C 92 ASN cc_start: 0.7891 (m-40) cc_final: 0.7409 (p0) REVERT: C 326 LYS cc_start: 0.8945 (OUTLIER) cc_final: 0.8597 (mtpt) REVERT: E 339 LYS cc_start: 0.8191 (tttp) cc_final: 0.7644 (mtmt) REVERT: B 412 VAL cc_start: 0.7247 (OUTLIER) cc_final: 0.6954 (p) REVERT: B 450 GLU cc_start: 0.8308 (mm-30) cc_final: 0.8012 (mm-30) REVERT: B 452 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8464 (tt0) REVERT: B 509 TYR cc_start: 0.8416 (m-80) cc_final: 0.8181 (m-80) REVERT: D 385 LEU cc_start: 0.8405 (mm) cc_final: 0.8122 (mt) REVERT: D 498 GLU cc_start: 0.7696 (mt-10) cc_final: 0.7482 (mt-10) REVERT: D 512 ASP cc_start: 0.7989 (m-30) cc_final: 0.7715 (m-30) REVERT: F 412 VAL cc_start: 0.7408 (OUTLIER) cc_final: 0.7133 (p) REVERT: F 435 ARG cc_start: 0.8601 (ttt180) cc_final: 0.8243 (ttt180) REVERT: F 438 GLU cc_start: 0.8425 (mm-30) cc_final: 0.8143 (mm-30) REVERT: F 512 ASP cc_start: 0.8043 (m-30) cc_final: 0.7633 (m-30) outliers start: 36 outliers final: 18 residues processed: 175 average time/residue: 0.5509 time to fit residues: 103.8898 Evaluate side-chains 160 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 138 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 99 CYS Chi-restraints excluded: chain C residue 6 ASP Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 99 CYS Chi-restraints excluded: chain C residue 326 LYS Chi-restraints excluded: chain E residue 99 CYS Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 415 SER Chi-restraints excluded: chain D residue 446 ILE Chi-restraints excluded: chain D residue 495 CYS Chi-restraints excluded: chain F residue 374 THR Chi-restraints excluded: chain F residue 379 THR Chi-restraints excluded: chain F residue 412 VAL Chi-restraints excluded: chain F residue 414 ASP Chi-restraints excluded: chain F residue 444 GLU Chi-restraints excluded: chain F residue 495 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 23 optimal weight: 4.9990 chunk 138 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 42 optimal weight: 0.0970 chunk 14 optimal weight: 1.9990 chunk 129 optimal weight: 7.9990 chunk 121 optimal weight: 1.9990 chunk 87 optimal weight: 0.0370 overall best weight: 1.4262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 ASN E 167 ASN B 369 HIS B 403 ASN B 442 GLN D 369 HIS D 403 ASN D 467 GLN F 369 HIS F 442 GLN F 490 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.119265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.098985 restraints weight = 14447.333| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 1.54 r_work: 0.3113 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11661 Z= 0.195 Angle : 0.640 9.612 15828 Z= 0.329 Chirality : 0.046 0.182 1824 Planarity : 0.005 0.046 2034 Dihedral : 5.447 30.877 1818 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.14 % Allowed : 11.76 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 aren not related in a simple way. whole: 0.56 (0.21), residues: 1470 helix: 2.13 (0.28), residues: 321 sheet: 0.23 (0.31), residues: 285 loop : -0.21 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 497 TYR 0.010 0.002 TYR E 265 PHE 0.017 0.002 PHE C 275 TRP 0.009 0.001 TRP E 196 HIS 0.006 0.001 HIS D 489 Details of bonding type rmsd covalent geometry : bond 0.00460 (11631) covalent geometry : angle 0.63277 (15756) SS BOND : bond 0.00261 ( 18) SS BOND : angle 1.14751 ( 36) hydrogen bonds : bond 0.05175 ( 460) hydrogen bonds : angle 5.18199 ( 1272) link_BETA1-4 : bond 0.00230 ( 6) link_BETA1-4 : angle 1.77534 ( 18) link_NAG-ASN : bond 0.00197 ( 6) link_NAG-ASN : angle 1.87275 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 148 time to evaluate : 0.445 Fit side-chains REVERT: A 92 ASN cc_start: 0.8159 (m-40) cc_final: 0.7478 (p0) REVERT: A 98 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.7007 (mmmt) REVERT: C 68 MET cc_start: 0.9195 (tpp) cc_final: 0.8958 (tpp) REVERT: C 92 ASN cc_start: 0.7860 (m-40) cc_final: 0.7282 (p0) REVERT: E 339 LYS cc_start: 0.8213 (tttp) cc_final: 0.7611 (mtmt) REVERT: B 412 VAL cc_start: 0.7293 (OUTLIER) cc_final: 0.7002 (p) REVERT: B 452 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.8367 (tt0) REVERT: D 364 MET cc_start: 0.1441 (OUTLIER) cc_final: 0.0512 (ppp) REVERT: D 498 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7421 (mt-10) REVERT: D 512 ASP cc_start: 0.8001 (m-30) cc_final: 0.7710 (m-30) REVERT: F 387 SER cc_start: 0.8557 (p) cc_final: 0.8261 (p) REVERT: F 512 ASP cc_start: 0.7980 (m-30) cc_final: 0.7522 (m-30) outliers start: 39 outliers final: 21 residues processed: 173 average time/residue: 0.5587 time to fit residues: 104.5779 Evaluate side-chains 166 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 141 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 98 LYS Chi-restraints excluded: chain A residue 99 CYS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain C residue 6 ASP Chi-restraints excluded: chain C residue 99 CYS Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 329 ARG Chi-restraints excluded: chain E residue 99 CYS Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain D residue 364 MET Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 415 SER Chi-restraints excluded: chain D residue 446 ILE Chi-restraints excluded: chain D residue 495 CYS Chi-restraints excluded: chain F residue 374 THR Chi-restraints excluded: chain F residue 379 THR Chi-restraints excluded: chain F residue 412 VAL Chi-restraints excluded: chain F residue 444 GLU Chi-restraints excluded: chain F residue 490 GLN Chi-restraints excluded: chain F residue 495 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 33 optimal weight: 7.9990 chunk 129 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 72 optimal weight: 0.7980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 ASN E 167 ASN E 181 HIS B 369 HIS D 403 ASN F 442 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.118454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.098225 restraints weight = 14359.599| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 1.53 r_work: 0.3102 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 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 : 0.005 0.034 11661 Z= 0.195 Angle : 0.626 9.580 15828 Z= 0.322 Chirality : 0.046 0.175 1824 Planarity : 0.005 0.047 2034 Dihedral : 5.442 30.592 1818 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.66 % Allowed : 12.96 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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 aren not related in a simple way. whole: 0.37 (0.22), residues: 1470 helix: 2.12 (0.28), residues: 321 sheet: -0.01 (0.31), residues: 291 loop : -0.36 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 497 TYR 0.010 0.002 TYR E 265 PHE 0.017 0.002 PHE C 275 TRP 0.008 0.001 TRP E 196 HIS 0.008 0.001 HIS F 489 Details of bonding type rmsd covalent geometry : bond 0.00461 (11631) covalent geometry : angle 0.61884 (15756) SS BOND : bond 0.00260 ( 18) SS BOND : angle 1.12215 ( 36) hydrogen bonds : bond 0.05113 ( 460) hydrogen bonds : angle 5.16385 ( 1272) link_BETA1-4 : bond 0.00199 ( 6) link_BETA1-4 : angle 1.71859 ( 18) link_NAG-ASN : bond 0.00152 ( 6) link_NAG-ASN : angle 1.88213 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 139 time to evaluate : 0.461 Fit side-chains REVERT: A 92 ASN cc_start: 0.8143 (m-40) cc_final: 0.7484 (p0) REVERT: A 98 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.7063 (mmmt) REVERT: C 16 LYS cc_start: 0.7940 (OUTLIER) cc_final: 0.7245 (tmtt) REVERT: C 68 MET cc_start: 0.9185 (tpp) cc_final: 0.8895 (tpp) REVERT: C 92 ASN cc_start: 0.7882 (m-40) cc_final: 0.7264 (p0) REVERT: E 92 ASN cc_start: 0.8140 (m-40) cc_final: 0.7482 (p0) REVERT: E 339 LYS cc_start: 0.8177 (tttp) cc_final: 0.7608 (mtmt) REVERT: B 412 VAL cc_start: 0.7402 (OUTLIER) cc_final: 0.7111 (p) REVERT: B 452 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8374 (tt0) REVERT: D 498 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7454 (mt-10) REVERT: D 512 ASP cc_start: 0.8064 (m-30) cc_final: 0.7710 (m-30) REVERT: F 387 SER cc_start: 0.8563 (p) cc_final: 0.8281 (p) REVERT: F 412 VAL cc_start: 0.7566 (OUTLIER) cc_final: 0.7293 (p) outliers start: 33 outliers final: 23 residues processed: 159 average time/residue: 0.5954 time to fit residues: 102.2480 Evaluate side-chains 161 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 133 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 98 LYS Chi-restraints excluded: chain A residue 99 CYS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain C residue 6 ASP Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 99 CYS Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 292 ASN Chi-restraints excluded: chain C residue 329 ARG Chi-restraints excluded: chain E residue 6 ASP Chi-restraints excluded: chain E residue 99 CYS Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 415 SER Chi-restraints excluded: chain D residue 446 ILE Chi-restraints excluded: chain D residue 495 CYS Chi-restraints excluded: chain D residue 500 VAL Chi-restraints excluded: chain F residue 364 MET Chi-restraints excluded: chain F residue 374 THR Chi-restraints excluded: chain F residue 379 THR Chi-restraints excluded: chain F residue 412 VAL Chi-restraints excluded: chain F residue 444 GLU Chi-restraints excluded: chain F residue 495 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 64 optimal weight: 3.9990 chunk 40 optimal weight: 0.5980 chunk 59 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 94 optimal weight: 0.0070 chunk 112 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 111 optimal weight: 0.7980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 143 ASN B 369 HIS D 401 ASN D 403 ASN F 442 GLN F 490 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.124117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.106199 restraints weight = 14753.868| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.33 r_work: 0.3244 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11661 Z= 0.121 Angle : 0.560 7.808 15828 Z= 0.288 Chirality : 0.043 0.164 1824 Planarity : 0.004 0.045 2034 Dihedral : 5.185 32.245 1818 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.82 % Allowed : 14.01 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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 aren not related in a simple way. whole: 0.46 (0.22), residues: 1470 helix: 2.35 (0.28), residues: 321 sheet: -0.10 (0.29), residues: 321 loop : -0.31 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 497 TYR 0.008 0.001 TYR A 313 PHE 0.015 0.002 PHE C 275 TRP 0.007 0.001 TRP A 327 HIS 0.005 0.001 HIS F 461 Details of bonding type rmsd covalent geometry : bond 0.00270 (11631) covalent geometry : angle 0.55390 (15756) SS BOND : bond 0.00193 ( 18) SS BOND : angle 0.93871 ( 36) hydrogen bonds : bond 0.04498 ( 460) hydrogen bonds : angle 4.96666 ( 1272) link_BETA1-4 : bond 0.00267 ( 6) link_BETA1-4 : angle 1.54380 ( 18) link_NAG-ASN : bond 0.00229 ( 6) link_NAG-ASN : angle 1.75301 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 148 time to evaluate : 0.564 Fit side-chains REVERT: A 92 ASN cc_start: 0.8194 (m-40) cc_final: 0.7791 (p0) REVERT: A 98 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.7353 (mmmt) REVERT: C 68 MET cc_start: 0.9228 (tpp) cc_final: 0.8978 (tpp) REVERT: C 92 ASN cc_start: 0.7970 (m-40) cc_final: 0.7517 (p0) REVERT: E 92 ASN cc_start: 0.8189 (m-40) cc_final: 0.7736 (p0) REVERT: E 339 LYS cc_start: 0.8140 (tttp) cc_final: 0.7759 (mtmt) REVERT: D 498 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7606 (mt-10) REVERT: D 512 ASP cc_start: 0.7902 (m-30) cc_final: 0.7610 (m-30) REVERT: F 364 MET cc_start: 0.1947 (OUTLIER) cc_final: 0.0988 (ppp) REVERT: F 387 SER cc_start: 0.8694 (p) cc_final: 0.8419 (p) REVERT: F 480 MET cc_start: 0.8626 (mtt) cc_final: 0.8190 (mtp) outliers start: 35 outliers final: 15 residues processed: 165 average time/residue: 0.5505 time to fit residues: 98.4233 Evaluate side-chains 156 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 139 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 98 LYS Chi-restraints excluded: chain A residue 99 CYS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain C residue 6 ASP Chi-restraints excluded: chain C residue 99 CYS Chi-restraints excluded: chain E residue 99 CYS Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 415 SER Chi-restraints excluded: chain D residue 446 ILE Chi-restraints excluded: chain D residue 495 CYS Chi-restraints excluded: chain F residue 364 MET Chi-restraints excluded: chain F residue 374 THR Chi-restraints excluded: chain F residue 495 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 38 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 138 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 114 optimal weight: 0.2980 chunk 100 optimal weight: 10.0000 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 369 HIS D 403 ASN F 403 ASN F 442 GLN F 490 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.121052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.102803 restraints weight = 14709.136| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.36 r_work: 0.3190 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 11661 Z= 0.212 Angle : 0.635 9.285 15828 Z= 0.325 Chirality : 0.046 0.180 1824 Planarity : 0.005 0.049 2034 Dihedral : 5.443 29.513 1818 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.09 % Allowed : 15.14 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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 aren not related in a simple way. whole: 0.36 (0.21), residues: 1470 helix: 2.23 (0.28), residues: 321 sheet: 0.12 (0.33), residues: 255 loop : -0.46 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 497 TYR 0.012 0.002 TYR E 265 PHE 0.015 0.002 PHE C 275 TRP 0.009 0.001 TRP E 196 HIS 0.006 0.001 HIS B 489 Details of bonding type rmsd covalent geometry : bond 0.00503 (11631) covalent geometry : angle 0.62815 (15756) SS BOND : bond 0.00250 ( 18) SS BOND : angle 1.01234 ( 36) hydrogen bonds : bond 0.05052 ( 460) hydrogen bonds : angle 5.12833 ( 1272) link_BETA1-4 : bond 0.00193 ( 6) link_BETA1-4 : angle 1.71292 ( 18) link_NAG-ASN : bond 0.00157 ( 6) link_NAG-ASN : angle 1.91419 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 0.548 Fit side-chains REVERT: A 92 ASN cc_start: 0.8191 (m-40) cc_final: 0.7694 (p0) REVERT: C 68 MET cc_start: 0.9223 (tpp) cc_final: 0.8997 (tpp) REVERT: C 92 ASN cc_start: 0.8022 (m-40) cc_final: 0.7483 (p0) REVERT: E 92 ASN cc_start: 0.8216 (m-40) cc_final: 0.7672 (p0) REVERT: E 339 LYS cc_start: 0.8267 (tttp) cc_final: 0.7738 (mtmt) REVERT: B 452 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8556 (tt0) REVERT: D 498 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7670 (mt-10) REVERT: D 512 ASP cc_start: 0.7894 (m-30) cc_final: 0.7536 (m-30) REVERT: F 364 MET cc_start: 0.2008 (OUTLIER) cc_final: 0.1049 (ppp) REVERT: F 387 SER cc_start: 0.8665 (p) cc_final: 0.8376 (p) outliers start: 26 outliers final: 18 residues processed: 157 average time/residue: 0.6290 time to fit residues: 106.7587 Evaluate side-chains 155 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 135 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 99 CYS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain C residue 6 ASP Chi-restraints excluded: chain C residue 99 CYS Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain E residue 99 CYS Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 415 SER Chi-restraints excluded: chain D residue 446 ILE Chi-restraints excluded: chain D residue 495 CYS Chi-restraints excluded: chain F residue 364 MET Chi-restraints excluded: chain F residue 374 THR Chi-restraints excluded: chain F residue 495 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 105 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 135 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN C 152 ASN E 100 ASN E 147 ASN D 403 ASN F 400 ASN F 442 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.121510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.102967 restraints weight = 14277.785| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.38 r_work: 0.3216 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11661 Z= 0.178 Angle : 0.606 8.739 15828 Z= 0.311 Chirality : 0.045 0.172 1824 Planarity : 0.005 0.050 2034 Dihedral : 5.392 29.852 1818 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.93 % Allowed : 15.30 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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 aren not related in a simple way. whole: 0.36 (0.22), residues: 1470 helix: 2.27 (0.28), residues: 321 sheet: -0.09 (0.31), residues: 291 loop : -0.40 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 497 TYR 0.009 0.002 TYR F 509 PHE 0.013 0.002 PHE A 275 TRP 0.008 0.001 TRP A 327 HIS 0.005 0.001 HIS F 461 Details of bonding type rmsd covalent geometry : bond 0.00420 (11631) covalent geometry : angle 0.59980 (15756) SS BOND : bond 0.00228 ( 18) SS BOND : angle 0.96122 ( 36) hydrogen bonds : bond 0.04865 ( 460) hydrogen bonds : angle 5.09761 ( 1272) link_BETA1-4 : bond 0.00199 ( 6) link_BETA1-4 : angle 1.65454 ( 18) link_NAG-ASN : bond 0.00179 ( 6) link_NAG-ASN : angle 1.89244 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 0.513 Fit side-chains REVERT: A 92 ASN cc_start: 0.8202 (m-40) cc_final: 0.7793 (p0) REVERT: C 68 MET cc_start: 0.9204 (tpp) cc_final: 0.8927 (tpp) REVERT: C 92 ASN cc_start: 0.8120 (m-40) cc_final: 0.7623 (p0) REVERT: E 92 ASN cc_start: 0.8290 (m-40) cc_final: 0.7806 (p0) REVERT: E 339 LYS cc_start: 0.8275 (tttp) cc_final: 0.7857 (mtmt) REVERT: B 452 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.8599 (tt0) REVERT: D 512 ASP cc_start: 0.7924 (m-30) cc_final: 0.7571 (m-30) REVERT: F 364 MET cc_start: 0.2355 (OUTLIER) cc_final: 0.1164 (ppp) REVERT: F 387 SER cc_start: 0.8717 (p) cc_final: 0.8447 (p) outliers start: 24 outliers final: 19 residues processed: 154 average time/residue: 0.6121 time to fit residues: 101.8004 Evaluate side-chains 156 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 99 CYS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain C residue 6 ASP Chi-restraints excluded: chain C residue 99 CYS Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain E residue 99 CYS Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 444 GLU Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain B residue 495 CYS Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 415 SER Chi-restraints excluded: chain D residue 446 ILE Chi-restraints excluded: chain D residue 495 CYS Chi-restraints excluded: chain F residue 364 MET Chi-restraints excluded: chain F residue 374 THR Chi-restraints excluded: chain F residue 495 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 109 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 96 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 142 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 400 ASN D 403 ASN F 403 ASN F 442 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.120795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.102186 restraints weight = 14276.937| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.38 r_work: 0.3203 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11661 Z= 0.200 Angle : 0.632 9.672 15828 Z= 0.323 Chirality : 0.046 0.199 1824 Planarity : 0.005 0.054 2034 Dihedral : 5.480 29.235 1818 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.09 % Allowed : 15.14 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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 aren not related in a simple way. whole: 0.30 (0.21), residues: 1470 helix: 2.14 (0.27), residues: 324 sheet: 0.11 (0.32), residues: 270 loop : -0.51 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 497 TYR 0.010 0.002 TYR E 265 PHE 0.012 0.002 PHE A 158 TRP 0.009 0.001 TRP E 196 HIS 0.005 0.001 HIS B 489 Details of bonding type rmsd covalent geometry : bond 0.00475 (11631) covalent geometry : angle 0.62597 (15756) SS BOND : bond 0.00238 ( 18) SS BOND : angle 0.96728 ( 36) hydrogen bonds : bond 0.04996 ( 460) hydrogen bonds : angle 5.15379 ( 1272) link_BETA1-4 : bond 0.00182 ( 6) link_BETA1-4 : angle 1.68906 ( 18) link_NAG-ASN : bond 0.00170 ( 6) link_NAG-ASN : angle 1.92200 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 0.494 Fit side-chains REVERT: A 92 ASN cc_start: 0.8203 (m-40) cc_final: 0.7783 (p0) REVERT: C 68 MET cc_start: 0.9201 (tpp) cc_final: 0.8928 (tpp) REVERT: C 92 ASN cc_start: 0.8110 (m-40) cc_final: 0.7622 (p0) REVERT: E 92 ASN cc_start: 0.8301 (m-40) cc_final: 0.7796 (p0) REVERT: E 339 LYS cc_start: 0.8311 (tttp) cc_final: 0.7873 (mtmt) REVERT: B 452 GLU cc_start: 0.8873 (OUTLIER) cc_final: 0.8620 (tt0) REVERT: D 512 ASP cc_start: 0.7927 (m-30) cc_final: 0.7550 (m-30) REVERT: F 364 MET cc_start: 0.2307 (OUTLIER) cc_final: 0.1124 (ppp) REVERT: F 413 THR cc_start: 0.8302 (OUTLIER) cc_final: 0.7981 (m) outliers start: 26 outliers final: 20 residues processed: 155 average time/residue: 0.5991 time to fit residues: 100.6042 Evaluate side-chains 157 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 134 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 99 CYS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain C residue 6 ASP Chi-restraints excluded: chain C residue 99 CYS Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain E residue 99 CYS Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 444 GLU Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain B residue 495 CYS Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 415 SER Chi-restraints excluded: chain D residue 446 ILE Chi-restraints excluded: chain D residue 495 CYS Chi-restraints excluded: chain F residue 364 MET Chi-restraints excluded: chain F residue 374 THR Chi-restraints excluded: chain F residue 413 THR Chi-restraints excluded: chain F residue 495 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 71 optimal weight: 0.2980 chunk 6 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 113 optimal weight: 0.0970 chunk 105 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 chunk 68 optimal weight: 0.0970 chunk 121 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 400 ASN F 442 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.125218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.107209 restraints weight = 14143.317| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.33 r_work: 0.3256 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11661 Z= 0.109 Angle : 0.562 10.020 15828 Z= 0.285 Chirality : 0.042 0.206 1824 Planarity : 0.005 0.053 2034 Dihedral : 5.141 34.010 1818 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.85 % Allowed : 15.30 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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 aren not related in a simple way. whole: 0.55 (0.22), residues: 1470 helix: 2.47 (0.28), residues: 321 sheet: 0.01 (0.31), residues: 306 loop : -0.30 (0.21), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 497 TYR 0.009 0.001 TYR F 509 PHE 0.014 0.001 PHE C 275 TRP 0.007 0.001 TRP A 193 HIS 0.005 0.001 HIS F 461 Details of bonding type rmsd covalent geometry : bond 0.00240 (11631) covalent geometry : angle 0.55595 (15756) SS BOND : bond 0.00185 ( 18) SS BOND : angle 0.93904 ( 36) hydrogen bonds : bond 0.04284 ( 460) hydrogen bonds : angle 4.89614 ( 1272) link_BETA1-4 : bond 0.00256 ( 6) link_BETA1-4 : angle 1.47314 ( 18) link_NAG-ASN : bond 0.00232 ( 6) link_NAG-ASN : angle 1.69497 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 143 time to evaluate : 0.431 Fit side-chains REVERT: A 20 ARG cc_start: 0.8185 (mtp180) cc_final: 0.7958 (mmm160) REVERT: A 92 ASN cc_start: 0.8189 (m-40) cc_final: 0.7821 (p0) REVERT: C 68 MET cc_start: 0.9191 (tpp) cc_final: 0.8932 (tpp) REVERT: C 92 ASN cc_start: 0.8061 (m-40) cc_final: 0.7632 (p0) REVERT: C 339 LYS cc_start: 0.8341 (mtpm) cc_final: 0.7936 (mtpt) REVERT: E 92 ASN cc_start: 0.8288 (m-40) cc_final: 0.7848 (p0) REVERT: E 339 LYS cc_start: 0.8168 (tttp) cc_final: 0.7779 (mtmt) REVERT: B 402 MET cc_start: 0.8499 (mtm) cc_final: 0.8297 (mtm) REVERT: D 364 MET cc_start: 0.2007 (tpp) cc_final: 0.1151 (pp-130) REVERT: D 445 MET cc_start: 0.8129 (mtp) cc_final: 0.7457 (mmp) REVERT: D 512 ASP cc_start: 0.7870 (m-30) cc_final: 0.7519 (m-30) REVERT: F 364 MET cc_start: 0.2286 (OUTLIER) cc_final: 0.1292 (ppp) REVERT: F 387 SER cc_start: 0.8806 (t) cc_final: 0.8276 (t) REVERT: F 413 THR cc_start: 0.8316 (OUTLIER) cc_final: 0.8073 (m) REVERT: F 480 MET cc_start: 0.8653 (mtt) cc_final: 0.8213 (mtp) outliers start: 23 outliers final: 18 residues processed: 158 average time/residue: 0.5453 time to fit residues: 93.3834 Evaluate side-chains 152 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 99 CYS Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain C residue 6 ASP Chi-restraints excluded: chain C residue 99 CYS Chi-restraints excluded: chain C residue 292 ASN Chi-restraints excluded: chain E residue 99 CYS Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 495 CYS Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 415 SER Chi-restraints excluded: chain D residue 495 CYS Chi-restraints excluded: chain F residue 364 MET Chi-restraints excluded: chain F residue 374 THR Chi-restraints excluded: chain F residue 413 THR Chi-restraints excluded: chain F residue 495 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 54 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 104 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 125 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 21 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 400 ASN F 442 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.121551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.102957 restraints weight = 14312.712| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.38 r_work: 0.3206 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 11661 Z= 0.200 Angle : 0.629 9.963 15828 Z= 0.321 Chirality : 0.046 0.208 1824 Planarity : 0.005 0.059 2034 Dihedral : 5.392 30.938 1818 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.61 % Allowed : 15.14 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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 aren not related in a simple way. whole: 0.33 (0.22), residues: 1470 helix: 2.20 (0.27), residues: 324 sheet: -0.07 (0.31), residues: 291 loop : -0.44 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 497 TYR 0.011 0.002 TYR E 265 PHE 0.012 0.002 PHE A 158 TRP 0.009 0.001 TRP E 196 HIS 0.005 0.001 HIS B 489 Details of bonding type rmsd covalent geometry : bond 0.00478 (11631) covalent geometry : angle 0.62353 (15756) SS BOND : bond 0.00237 ( 18) SS BOND : angle 0.95747 ( 36) hydrogen bonds : bond 0.04924 ( 460) hydrogen bonds : angle 5.07183 ( 1272) link_BETA1-4 : bond 0.00181 ( 6) link_BETA1-4 : angle 1.67235 ( 18) link_NAG-ASN : bond 0.00168 ( 6) link_NAG-ASN : angle 1.86040 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3692.99 seconds wall clock time: 63 minutes 57.77 seconds (3837.77 seconds total)