Starting phenix.real_space_refine on Tue Aug 4 19:29:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vck_64956/08_2026/9vck_64956.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vck_64956/08_2026/9vck_64956.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vck_64956/08_2026/9vck_64956.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vck_64956/08_2026/9vck_64956.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vck_64956/08_2026/9vck_64956.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vck_64956/08_2026/9vck_64956.map" } resolution = 4.22 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= -0.027 sd= 0.302 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: 8 Type Number sf(0) Gaussians Ca 2 9.91 5 Zn 5 6.06 5 P 55 5.49 5 S 52 5.16 5 C 3742 2.51 5 N 1052 2.21 5 O 1304 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6213 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 954 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 7, 'TRANS': 123} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 4089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 4089 Classifications: {'peptide': 512} Link IDs: {'PTRANS': 26, 'TRANS': 485} Chain breaks: 1 Chain: "P" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 546 Classifications: {'RNA': 26} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 12, 'rna3p_pyr': 13} Link IDs: {'rna3p': 25} Chain: "T" Number of atoms: 596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 596 Classifications: {'RNA': 28} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 14, 'rna3p_pyr': 13} Link IDs: {'rna2p': 1, 'rna3p': 26} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' CA': 2, ' ZN': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "P" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'K5X': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 519 SG CYS A 74 37.415 23.243 43.824 1.00 77.90 S ATOM 545 SG CYS A 77 40.888 24.213 43.292 1.00 75.14 S ATOM 650 SG CYS A 90 39.318 21.277 41.574 1.00 85.58 S ATOM 934 SG CYS A 128 21.878 11.449 33.923 1.00117.96 S ATOM 946 SG CYS A 130 20.962 8.345 32.806 1.00116.65 S ATOM 2580 SG CYS B 207 34.584 19.970 75.504 1.00 86.92 S ATOM 2600 SG CYS B 210 32.599 20.657 79.257 1.00 92.82 S ATOM 2721 SG CYS B 226 35.423 22.304 77.955 1.00 86.86 S ATOM 3151 SG CYS B 279 50.116 49.845 80.260 1.00 86.02 S ATOM 4541 SG CYS B 452 30.660 33.991 128.193 1.00272.39 S ATOM 4697 SG CYS B 484 32.422 33.038 125.887 1.00256.35 S Time building chain proxies: 1.62, per 1000 atoms: 0.26 Number of scatterers: 6213 At special positions: 0 Unit cell: (78.85, 98.77, 139.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 5 29.99 Ca 2 19.99 S 52 16.00 P 55 15.00 F 1 9.00 O 1304 8.00 N 1052 7.00 C 3742 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.44 Conformation dependent library (CDL) restraints added in 348.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 201 " pdb="ZN ZN A 201 " - pdb=" NE2 HIS A 83 " pdb="ZN ZN A 201 " - pdb=" SG CYS A 90 " pdb="ZN ZN A 201 " - pdb=" SG CYS A 74 " pdb="ZN ZN A 201 " - pdb=" SG CYS A 77 " pdb=" ZN A 202 " pdb="ZN ZN A 202 " - pdb=" SG CYS A 128 " pdb="ZN ZN A 202 " - pdb=" SG CYS A 130 " pdb=" ZN B 603 " pdb="ZN ZN B 603 " - pdb=" ND1 HIS B 229 " pdb="ZN ZN B 603 " - pdb=" SG CYS B 207 " pdb="ZN ZN B 603 " - pdb=" SG CYS B 226 " pdb="ZN ZN B 603 " - pdb=" SG CYS B 210 " pdb=" ZN B 604 " pdb="ZN ZN B 604 " - pdb=" NE2 HIS B 257 " pdb="ZN ZN B 604 " - pdb=" ND1 HIS B 264 " pdb="ZN ZN B 604 " - pdb=" SG CYS B 279 " pdb=" ZN B 605 " pdb="ZN ZN B 605 " - pdb=" ND1 HIS B 487 " pdb="ZN ZN B 605 " - pdb=" SG CYS B 452 " pdb="ZN ZN B 605 " - pdb=" SG CYS B 484 " Number of angles added : 6 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1200 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 8 sheets defined 28.6% alpha, 15.1% beta 21 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 7 through 9 No H-bonds generated for 'chain 'A' and resid 7 through 9' Processing helix chain 'A' and resid 10 through 19 removed outlier: 3.536A pdb=" N PHE A 19 " --> pdb=" O SER A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 33 removed outlier: 3.768A pdb=" N SER A 33 " --> pdb=" O ASP A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 74 removed outlier: 4.001A pdb=" N CYS A 74 " --> pdb=" O GLY A 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 70 through 74' Processing helix chain 'A' and resid 74 through 80 Processing helix chain 'A' and resid 85 through 89 removed outlier: 3.926A pdb=" N GLY A 88 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N PHE A 89 " --> pdb=" O PRO A 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 85 through 89' Processing helix chain 'A' and resid 106 through 114 removed outlier: 3.768A pdb=" N PHE A 110 " --> pdb=" O ASP A 106 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THR A 111 " --> pdb=" O PRO A 107 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU A 112 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 82 Processing helix chain 'B' and resid 158 through 174 removed outlier: 3.755A pdb=" N ILE B 164 " --> pdb=" O ASN B 160 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP B 172 " --> pdb=" O GLN B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 177 No H-bonds generated for 'chain 'B' and resid 175 through 177' Processing helix chain 'B' and resid 191 through 196 Processing helix chain 'B' and resid 245 through 248 removed outlier: 3.564A pdb=" N GLY B 248 " --> pdb=" O GLN B 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 245 through 248' Processing helix chain 'B' and resid 252 through 258 removed outlier: 4.263A pdb=" N ASN B 256 " --> pdb=" O ASN B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 286 removed outlier: 3.637A pdb=" N MET B 276 " --> pdb=" O CYS B 272 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA B 281 " --> pdb=" O THR B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 325 removed outlier: 3.820A pdb=" N LYS B 318 " --> pdb=" O HIS B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 374 Processing helix chain 'B' and resid 432 through 437 removed outlier: 3.728A pdb=" N VAL B 437 " --> pdb=" O SER B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 480 Processing helix chain 'B' and resid 487 through 505 Processing helix chain 'B' and resid 516 through 523 removed outlier: 4.048A pdb=" N ASN B 521 " --> pdb=" O ASN B 518 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 55 through 56 Processing sheet with id=AA2, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'B' and resid 104 through 111 removed outlier: 7.267A pdb=" N ASN B 104 " --> pdb=" O ALA B 96 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ALA B 96 " --> pdb=" O ASN B 104 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N CYS B 94 " --> pdb=" O PRO B 106 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS B 139 " --> pdb=" O HIS B 95 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 104 through 111 removed outlier: 7.267A pdb=" N ASN B 104 " --> pdb=" O ALA B 96 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ALA B 96 " --> pdb=" O ASN B 104 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N CYS B 94 " --> pdb=" O PRO B 106 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 217 through 218 removed outlier: 3.554A pdb=" N SER B 218 " --> pdb=" O THR B 223 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N THR B 223 " --> pdb=" O SER B 218 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 364 through 365 removed outlier: 7.250A pdb=" N LEU B 329 " --> pdb=" O LYS B 349 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N TYR B 351 " --> pdb=" O LEU B 329 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ASP B 331 " --> pdb=" O TYR B 351 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N TRP B 385 " --> pdb=" O ILE B 332 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N CYS B 382 " --> pdb=" O ILE B 397 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N CYS B 399 " --> pdb=" O CYS B 382 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N PHE B 384 " --> pdb=" O CYS B 399 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N PHE B 401 " --> pdb=" O PHE B 384 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N SER B 396 " --> pdb=" O TYR B 511 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 410 through 412 Processing sheet with id=AA8, first strand: chain 'B' and resid 446 through 447 removed outlier: 6.199A pdb=" N TYR B 446 " --> pdb=" O ILE B 474 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 138 hydrogen bonds defined for protein. 381 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 43 hydrogen bonds 66 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 1.08 Time building geometry restraints manager: 0.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.03 - 1.18: 2 1.18 - 1.34: 1817 1.34 - 1.50: 2277 1.50 - 1.65: 2315 1.65 - 1.81: 68 Bond restraints: 6479 Sorted by residual: bond pdb=" C HIS B 268 " pdb=" O HIS B 268 " ideal model delta sigma weight residual 1.237 1.044 0.193 1.10e-02 8.26e+03 3.07e+02 bond pdb=" C HIS B 95 " pdb=" O HIS B 95 " ideal model delta sigma weight residual 1.234 1.027 0.207 1.22e-02 6.72e+03 2.89e+02 bond pdb=" C02 K5X P 101 " pdb=" C04 K5X P 101 " ideal model delta sigma weight residual 1.561 1.298 0.263 2.00e-02 2.50e+03 1.73e+02 bond pdb=" C HIS B 268 " pdb=" N VAL B 269 " ideal model delta sigma weight residual 1.335 1.207 0.128 1.18e-02 7.18e+03 1.17e+02 bond pdb=" CA HIS B 268 " pdb=" CB HIS B 268 " ideal model delta sigma weight residual 1.535 1.270 0.265 2.75e-02 1.32e+03 9.28e+01 ... (remaining 6474 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.84: 9024 5.84 - 11.69: 24 11.69 - 17.53: 3 17.53 - 23.38: 3 23.38 - 29.22: 3 Bond angle restraints: 9057 Sorted by residual: angle pdb=" N TYR B 237 " pdb=" CA TYR B 237 " pdb=" C TYR B 237 " ideal model delta sigma weight residual 110.97 138.35 -27.38 1.09e+00 8.42e-01 6.31e+02 angle pdb=" C PHE B 190 " pdb=" CA PHE B 190 " pdb=" CB PHE B 190 " ideal model delta sigma weight residual 111.91 82.69 29.22 1.52e+00 4.33e-01 3.70e+02 angle pdb=" N ASN B 238 " pdb=" CA ASN B 238 " pdb=" CB ASN B 238 " ideal model delta sigma weight residual 110.37 132.69 -22.32 1.78e+00 3.16e-01 1.57e+02 angle pdb=" O3' G T 7 " pdb=" C3' G T 7 " pdb=" C2' G T 7 " ideal model delta sigma weight residual 113.70 95.99 17.71 1.60e+00 3.91e-01 1.23e+02 angle pdb=" N ASN B 238 " pdb=" CA ASN B 238 " pdb=" C ASN B 238 " ideal model delta sigma weight residual 109.81 89.15 20.66 2.21e+00 2.05e-01 8.74e+01 ... (remaining 9052 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.63: 3507 23.63 - 47.26: 255 47.26 - 70.89: 91 70.89 - 94.52: 10 94.52 - 118.15: 4 Dihedral angle restraints: 3867 sinusoidal: 1997 harmonic: 1870 Sorted by residual: dihedral pdb=" C PHE B 190 " pdb=" N PHE B 190 " pdb=" CA PHE B 190 " pdb=" CB PHE B 190 " ideal model delta harmonic sigma weight residual -122.60 -85.39 -37.21 0 2.50e+00 1.60e-01 2.21e+02 dihedral pdb=" N TYR B 237 " pdb=" C TYR B 237 " pdb=" CA TYR B 237 " pdb=" CB TYR B 237 " ideal model delta harmonic sigma weight residual 122.80 148.71 -25.91 0 2.50e+00 1.60e-01 1.07e+02 dihedral pdb=" C TYR B 237 " pdb=" N TYR B 237 " pdb=" CA TYR B 237 " pdb=" CB TYR B 237 " ideal model delta harmonic sigma weight residual -122.60 -147.69 25.09 0 2.50e+00 1.60e-01 1.01e+02 ... (remaining 3864 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.277: 1038 0.277 - 0.554: 1 0.554 - 0.831: 1 0.831 - 1.108: 1 1.108 - 1.385: 1 Chirality restraints: 1042 Sorted by residual: chirality pdb=" CA TYR B 237 " pdb=" N TYR B 237 " pdb=" C TYR B 237 " pdb=" CB TYR B 237 " both_signs ideal model delta sigma weight residual False 2.51 1.13 1.38 2.00e-01 2.50e+01 4.79e+01 chirality pdb=" CA HIS B 268 " pdb=" N HIS B 268 " pdb=" C HIS B 268 " pdb=" CB HIS B 268 " both_signs ideal model delta sigma weight residual False 2.51 1.67 0.84 2.00e-01 2.50e+01 1.76e+01 chirality pdb=" CA PHE B 190 " pdb=" N PHE B 190 " pdb=" C PHE B 190 " pdb=" CB PHE B 190 " both_signs ideal model delta sigma weight residual False 2.51 3.16 -0.65 2.00e-01 2.50e+01 1.06e+01 ... (remaining 1039 not shown) Planarity restraints: 959 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS B 95 " 0.048 2.00e-02 2.50e+03 1.04e-01 1.08e+02 pdb=" C HIS B 95 " -0.179 2.00e-02 2.50e+03 pdb=" O HIS B 95 " 0.075 2.00e-02 2.50e+03 pdb=" N ALA B 96 " 0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS B 268 " -0.014 2.00e-02 2.50e+03 3.05e-02 9.30e+00 pdb=" C HIS B 268 " 0.053 2.00e-02 2.50e+03 pdb=" O HIS B 268 " -0.021 2.00e-02 2.50e+03 pdb=" N VAL B 269 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS B 285 " -0.015 2.00e-02 2.50e+03 3.01e-02 9.03e+00 pdb=" C CYS B 285 " 0.052 2.00e-02 2.50e+03 pdb=" O CYS B 285 " -0.019 2.00e-02 2.50e+03 pdb=" N PHE B 286 " -0.018 2.00e-02 2.50e+03 ... (remaining 956 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.25: 17 2.25 - 2.91: 2691 2.91 - 3.58: 9182 3.58 - 4.24: 15302 4.24 - 4.90: 22936 Nonbonded interactions: 50128 Sorted by model distance: nonbonded pdb=" O CYS B 285 " pdb=" NH1 ARG B 289 " model vdw 1.589 3.120 nonbonded pdb=" O LYS B 200 " pdb=" O TYR B 237 " model vdw 1.653 3.040 nonbonded pdb=" OE2 GLU B 191 " pdb="CA CA B 602 " model vdw 1.770 2.510 nonbonded pdb=" OD2 ASP B 90 " pdb="CA CA B 601 " model vdw 1.918 2.510 nonbonded pdb=" O PHE B 190 " pdb=" CB PHE B 190 " model vdw 2.014 2.752 ... (remaining 50123 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 group one per residue 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: 4.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.470 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 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 : 0.014 0.626 6496 Z= 0.675 Angle : 1.182 29.223 9063 Z= 0.698 Chirality : 0.079 1.385 1042 Planarity : 0.006 0.104 959 Dihedral : 17.949 118.154 2667 Min Nonbonded Distance : 1.589 Molprobity Statistics. All-atom Clashscore : 19.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 0.36 % Allowed : 7.04 % Favored : 92.60 % Cbeta Deviations : 0.83 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -3.56 (0.29), residues: 637 helix: -2.05 (0.38), residues: 139 sheet: -3.02 (0.50), residues: 69 loop : -2.50 (0.27), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 310 TYR 0.015 0.001 TYR B 235 PHE 0.017 0.002 PHE B 133 TRP 0.027 0.002 TRP B 348 HIS 0.013 0.002 HIS B 283 Details of bonding type rmsd/Z covalent geometry : bond 0.01025 / 0.60 ( 6479) covalent geometry : angle 1.13208 / 0.69 ( 9057) hydrogen bonds : bond 0.30553 / 20.10 ( 177) hydrogen bonds : angle 7.79047 / 5.49 ( 447) metal coordination : bond 0.18370 / 12.83 ( 16) metal coordination : angle 13.26123 / 6.56 ( 6) Misc. bond : bond 0.03232 / 1.54 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 102 time to evaluate : 0.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 GLU cc_start: 0.7593 (tp30) cc_final: 0.7377 (mm-30) REVERT: A 68 PHE cc_start: 0.7894 (m-80) cc_final: 0.6963 (m-10) REVERT: B 57 MET cc_start: 0.8524 (mmm) cc_final: 0.8251 (mmm) REVERT: B 350 PHE cc_start: 0.7858 (m-10) cc_final: 0.6763 (m-10) REVERT: B 500 MET cc_start: 0.8653 (ttp) cc_final: 0.8411 (ttp) outliers start: 2 outliers final: 0 residues processed: 103 average time/residue: 0.1060 time to fit residues: 13.3110 Evaluate side-chains 68 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.4980 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.4980 chunk 27 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 48 HIS A 53 GLN B 71 ASN B 354 GLN ** B 486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.052176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.041816 restraints weight = 37592.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.042920 restraints weight = 20009.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.043645 restraints weight = 12905.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.044128 restraints weight = 9594.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.044371 restraints weight = 7838.360| |-----------------------------------------------------------------------------| r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6496 Z= 0.179 Angle : 0.718 10.630 9063 Z= 0.376 Chirality : 0.045 0.209 1042 Planarity : 0.006 0.065 959 Dihedral : 17.610 124.875 1519 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 0.18 % Allowed : 7.22 % Favored : 92.60 % 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 are not related in a simple way. whole: -2.79 (0.30), residues: 637 helix: -1.27 (0.39), residues: 154 sheet: -2.21 (0.57), residues: 65 loop : -2.13 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 476 TYR 0.028 0.002 TYR B 351 PHE 0.027 0.002 PHE A 68 TRP 0.019 0.002 TRP B 348 HIS 0.009 0.002 HIS B 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.18 ( 6479) covalent geometry : angle 0.71459 / 0.38 ( 9057) hydrogen bonds : bond 0.10380 / 7.75 ( 177) hydrogen bonds : angle 5.43469 / 3.78 ( 447) metal coordination : bond 0.00637 / 0.45 ( 16) metal coordination : angle 2.81468 / 1.51 ( 6) Misc. bond : bond 0.00555 / 0.26 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 89 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 PHE cc_start: 0.7892 (m-80) cc_final: 0.7546 (m-80) REVERT: B 72 MET cc_start: 0.8895 (mtm) cc_final: 0.8669 (mtm) outliers start: 1 outliers final: 0 residues processed: 90 average time/residue: 0.0822 time to fit residues: 9.5084 Evaluate side-chains 70 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 12 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 13 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 60 optimal weight: 10.0000 chunk 33 optimal weight: 0.7980 chunk 61 optimal weight: 0.5980 chunk 24 optimal weight: 0.0870 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 256 ASN B 306 ASN ** B 486 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 = 0.3207 r_free = 0.3207 target = 0.051866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.041458 restraints weight = 36716.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.042480 restraints weight = 20049.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.043177 restraints weight = 13185.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.043613 restraints weight = 9954.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.043836 restraints weight = 8297.774| |-----------------------------------------------------------------------------| r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6496 Z= 0.134 Angle : 0.621 9.719 9063 Z= 0.325 Chirality : 0.041 0.184 1042 Planarity : 0.005 0.049 959 Dihedral : 17.302 123.154 1519 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % 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 are not related in a simple way. whole: -2.36 (0.31), residues: 637 helix: -0.73 (0.40), residues: 154 sheet: -2.12 (0.57), residues: 65 loop : -1.89 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 78 TYR 0.028 0.002 TYR B 351 PHE 0.017 0.002 PHE B 367 TRP 0.024 0.002 TRP B 348 HIS 0.005 0.001 HIS B 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 ( 6479) covalent geometry : angle 0.61860 / 0.33 ( 9057) hydrogen bonds : bond 0.10266 / 7.77 ( 177) hydrogen bonds : angle 4.97722 / 3.45 ( 447) metal coordination : bond 0.00287 / 0.19 ( 16) metal coordination : angle 2.29548 / 1.25 ( 6) Misc. bond : bond 0.00310 / 0.15 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 PHE cc_start: 0.7894 (m-80) cc_final: 0.7649 (m-80) REVERT: B 57 MET cc_start: 0.8372 (mmm) cc_final: 0.7280 (mmm) REVERT: B 350 PHE cc_start: 0.7090 (m-10) cc_final: 0.6508 (m-10) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.0773 time to fit residues: 8.5572 Evaluate side-chains 63 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 6 optimal weight: 6.9990 chunk 8 optimal weight: 0.0770 chunk 40 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 overall best weight: 0.7538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.051314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.040832 restraints weight = 36567.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.041881 restraints weight = 19686.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.042590 restraints weight = 12907.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.043011 restraints weight = 9673.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.043341 restraints weight = 8038.557| |-----------------------------------------------------------------------------| r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6496 Z= 0.136 Angle : 0.606 10.135 9063 Z= 0.316 Chirality : 0.042 0.348 1042 Planarity : 0.005 0.054 959 Dihedral : 16.993 125.525 1519 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % 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 are not related in a simple way. whole: -2.17 (0.32), residues: 637 helix: -0.27 (0.41), residues: 154 sheet: -2.23 (0.53), residues: 75 loop : -1.83 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 84 TYR 0.016 0.001 TYR B 420 PHE 0.015 0.002 PHE A 89 TRP 0.024 0.002 TRP B 348 HIS 0.005 0.001 HIS B 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 ( 6479) covalent geometry : angle 0.60429 / 0.32 ( 9057) hydrogen bonds : bond 0.09557 / 7.29 ( 177) hydrogen bonds : angle 4.83130 / 3.33 ( 447) metal coordination : bond 0.00329 / 0.21 ( 16) metal coordination : angle 1.99952 / 1.13 ( 6) Misc. bond : bond 0.00207 / 0.10 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 PHE cc_start: 0.7780 (m-80) cc_final: 0.7352 (m-80) REVERT: A 85 ASN cc_start: 0.8268 (p0) cc_final: 0.7815 (p0) REVERT: B 285 CYS cc_start: 0.7879 (m) cc_final: 0.7633 (p) REVERT: B 350 PHE cc_start: 0.7255 (m-10) cc_final: 0.6209 (m-10) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.0762 time to fit residues: 8.8932 Evaluate side-chains 65 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 40 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 11 optimal weight: 0.0170 chunk 67 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 12 optimal weight: 0.5980 chunk 35 optimal weight: 0.0070 overall best weight: 0.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.050773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.040329 restraints weight = 36662.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.041366 restraints weight = 19742.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.042046 restraints weight = 13038.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.042492 restraints weight = 9892.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.042733 restraints weight = 8206.803| |-----------------------------------------------------------------------------| r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6496 Z= 0.128 Angle : 0.591 8.166 9063 Z= 0.306 Chirality : 0.041 0.218 1042 Planarity : 0.005 0.050 959 Dihedral : 16.855 127.658 1519 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % 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 are not related in a simple way. whole: -1.96 (0.31), residues: 637 helix: 0.04 (0.42), residues: 152 sheet: -2.05 (0.53), residues: 75 loop : -1.76 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 78 TYR 0.012 0.001 TYR B 420 PHE 0.023 0.002 PHE A 89 TRP 0.022 0.002 TRP B 348 HIS 0.004 0.001 HIS B 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 ( 6479) covalent geometry : angle 0.59030 / 0.31 ( 9057) hydrogen bonds : bond 0.09459 / 7.20 ( 177) hydrogen bonds : angle 4.72265 / 3.27 ( 447) metal coordination : bond 0.00295 / 0.17 ( 16) metal coordination : angle 1.46933 / 0.78 ( 6) Misc. bond : bond 0.00139 / 0.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 ASN cc_start: 0.8291 (p0) cc_final: 0.7679 (p0) REVERT: A 89 PHE cc_start: 0.7511 (m-80) cc_final: 0.7236 (m-10) REVERT: B 57 MET cc_start: 0.8365 (mmm) cc_final: 0.7209 (mmm) REVERT: B 285 CYS cc_start: 0.7802 (m) cc_final: 0.7487 (p) REVERT: B 350 PHE cc_start: 0.7175 (m-10) cc_final: 0.6115 (m-10) REVERT: B 415 ASP cc_start: 0.7449 (m-30) cc_final: 0.7193 (m-30) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.0773 time to fit residues: 8.5535 Evaluate side-chains 65 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 0 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 48 optimal weight: 0.0870 chunk 54 optimal weight: 0.5980 chunk 8 optimal weight: 0.0970 chunk 32 optimal weight: 0.7980 chunk 66 optimal weight: 9.9990 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 10 ASN ** A 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 486 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.051222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.040702 restraints weight = 36769.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.041798 restraints weight = 19620.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.042517 restraints weight = 12758.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.042988 restraints weight = 9554.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.043209 restraints weight = 7825.559| |-----------------------------------------------------------------------------| r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 6496 Z= 0.112 Angle : 0.583 12.132 9063 Z= 0.295 Chirality : 0.039 0.184 1042 Planarity : 0.004 0.047 959 Dihedral : 16.702 130.749 1519 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % 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 are not related in a simple way. whole: -1.82 (0.32), residues: 637 helix: 0.14 (0.43), residues: 151 sheet: -1.94 (0.52), residues: 75 loop : -1.66 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 212 TYR 0.029 0.001 TYR B 351 PHE 0.010 0.001 PHE A 68 TRP 0.029 0.002 TRP B 348 HIS 0.009 0.001 HIS B 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 ( 6479) covalent geometry : angle 0.58202 / 0.30 ( 9057) hydrogen bonds : bond 0.09277 / 7.07 ( 177) hydrogen bonds : angle 4.65225 / 3.23 ( 447) metal coordination : bond 0.00692 / 0.50 ( 16) metal coordination : angle 1.38456 / 0.69 ( 6) Misc. bond : bond 0.00145 / 0.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 PHE cc_start: 0.7513 (m-80) cc_final: 0.6601 (m-80) REVERT: A 85 ASN cc_start: 0.8336 (p0) cc_final: 0.7921 (p0) REVERT: B 57 MET cc_start: 0.8323 (mmm) cc_final: 0.7199 (mmm) REVERT: B 285 CYS cc_start: 0.7741 (m) cc_final: 0.7459 (p) REVERT: B 350 PHE cc_start: 0.7175 (m-80) cc_final: 0.6131 (m-10) REVERT: B 415 ASP cc_start: 0.7612 (m-30) cc_final: 0.7231 (m-30) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.0725 time to fit residues: 7.9050 Evaluate side-chains 66 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 30 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 64 optimal weight: 20.0000 chunk 56 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 67 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 chunk 2 optimal weight: 0.2980 chunk 35 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.049636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.039045 restraints weight = 36632.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.040108 restraints weight = 19738.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.040805 restraints weight = 12914.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.041193 restraints weight = 9701.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.041539 restraints weight = 8133.102| |-----------------------------------------------------------------------------| r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.4187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6496 Z= 0.145 Angle : 0.604 10.119 9063 Z= 0.308 Chirality : 0.040 0.181 1042 Planarity : 0.005 0.049 959 Dihedral : 16.651 136.887 1519 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % 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 are not related in a simple way. whole: -1.60 (0.32), residues: 637 helix: 0.35 (0.43), residues: 152 sheet: -1.72 (0.50), residues: 81 loop : -1.54 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 84 TYR 0.011 0.001 TYR B 447 PHE 0.017 0.002 PHE B 523 TRP 0.027 0.002 TRP B 348 HIS 0.004 0.001 HIS A 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.15 ( 6479) covalent geometry : angle 0.60182 / 0.31 ( 9057) hydrogen bonds : bond 0.09290 / 7.01 ( 177) hydrogen bonds : angle 4.75237 / 3.30 ( 447) metal coordination : bond 0.00387 / 0.23 ( 16) metal coordination : angle 2.18832 / 1.00 ( 6) Misc. bond : bond 0.00129 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 ASN cc_start: 0.8380 (p0) cc_final: 0.7971 (p0) REVERT: B 49 MET cc_start: 0.8128 (ppp) cc_final: 0.7813 (ppp) REVERT: B 57 MET cc_start: 0.8314 (mmm) cc_final: 0.7125 (mmm) REVERT: B 285 CYS cc_start: 0.7753 (m) cc_final: 0.7541 (p) REVERT: B 350 PHE cc_start: 0.7176 (m-80) cc_final: 0.6461 (m-10) REVERT: B 415 ASP cc_start: 0.7623 (m-30) cc_final: 0.7248 (m-30) REVERT: B 433 LYS cc_start: 0.9251 (pptt) cc_final: 0.9036 (pptt) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.0798 time to fit residues: 8.2386 Evaluate side-chains 64 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 16 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 2 optimal weight: 0.0970 chunk 24 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.049958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.039380 restraints weight = 36679.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.040454 restraints weight = 19469.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.041172 restraints weight = 12665.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.041639 restraints weight = 9493.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.041857 restraints weight = 7812.676| |-----------------------------------------------------------------------------| r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.4361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6496 Z= 0.124 Angle : 0.608 9.811 9063 Z= 0.307 Chirality : 0.041 0.402 1042 Planarity : 0.004 0.049 959 Dihedral : 16.620 139.883 1519 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % 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 are not related in a simple way. whole: -1.57 (0.32), residues: 637 helix: 0.32 (0.43), residues: 152 sheet: -1.65 (0.53), residues: 75 loop : -1.51 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 476 TYR 0.010 0.001 TYR B 420 PHE 0.012 0.001 PHE B 350 TRP 0.031 0.002 TRP B 348 HIS 0.009 0.001 HIS B 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 6479) covalent geometry : angle 0.60718 / 0.31 ( 9057) hydrogen bonds : bond 0.09136 / 6.93 ( 177) hydrogen bonds : angle 4.70117 / 3.27 ( 447) metal coordination : bond 0.00304 / 0.18 ( 16) metal coordination : angle 0.99623 / 0.50 ( 6) Misc. bond : bond 0.00111 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 PHE cc_start: 0.7513 (m-80) cc_final: 0.7106 (m-80) REVERT: A 85 ASN cc_start: 0.8373 (p0) cc_final: 0.7964 (p0) REVERT: B 57 MET cc_start: 0.8328 (mmm) cc_final: 0.7199 (mmm) REVERT: B 285 CYS cc_start: 0.7728 (m) cc_final: 0.7470 (p) REVERT: B 350 PHE cc_start: 0.7180 (m-80) cc_final: 0.6474 (m-10) REVERT: B 415 ASP cc_start: 0.7587 (m-30) cc_final: 0.7248 (m-30) REVERT: B 433 LYS cc_start: 0.9286 (pptt) cc_final: 0.9049 (pptt) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.0737 time to fit residues: 7.6615 Evaluate side-chains 65 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 26 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 52 optimal weight: 0.2980 chunk 19 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 4 optimal weight: 0.0980 chunk 27 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 GLN ** B 486 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 = 0.3160 r_free = 0.3160 target = 0.050278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.039639 restraints weight = 36520.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.040712 restraints weight = 19292.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.041445 restraints weight = 12580.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.041887 restraints weight = 9396.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.042094 restraints weight = 7742.987| |-----------------------------------------------------------------------------| r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.4547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6496 Z= 0.114 Angle : 0.583 10.013 9063 Z= 0.294 Chirality : 0.041 0.362 1042 Planarity : 0.004 0.048 959 Dihedral : 16.550 144.429 1519 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % 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 are not related in a simple way. whole: -1.42 (0.32), residues: 637 helix: 0.47 (0.44), residues: 152 sheet: -1.40 (0.54), residues: 75 loop : -1.46 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 81 TYR 0.018 0.001 TYR B 351 PHE 0.015 0.002 PHE A 68 TRP 0.031 0.002 TRP B 348 HIS 0.010 0.001 HIS B 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 ( 6479) covalent geometry : angle 0.58268 / 0.29 ( 9057) hydrogen bonds : bond 0.09008 / 6.84 ( 177) hydrogen bonds : angle 4.62247 / 3.20 ( 447) metal coordination : bond 0.00836 / 0.38 ( 16) metal coordination : angle 1.06250 / 0.56 ( 6) Misc. bond : bond 0.00114 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 MET cc_start: 0.8120 (ppp) cc_final: 0.7843 (ppp) REVERT: B 57 MET cc_start: 0.8321 (mmm) cc_final: 0.7182 (mmm) REVERT: B 350 PHE cc_start: 0.7191 (m-80) cc_final: 0.6717 (m-10) REVERT: B 415 ASP cc_start: 0.7625 (m-30) cc_final: 0.7289 (m-30) REVERT: B 433 LYS cc_start: 0.9286 (pptt) cc_final: 0.9070 (pptt) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.0744 time to fit residues: 7.9139 Evaluate side-chains 64 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 47 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 67 optimal weight: 8.9990 chunk 18 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 GLN ** B 486 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 = 0.3144 r_free = 0.3144 target = 0.049804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.039294 restraints weight = 37057.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.040347 restraints weight = 19579.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.041058 restraints weight = 12907.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.041529 restraints weight = 9703.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.041777 restraints weight = 8017.259| |-----------------------------------------------------------------------------| r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.4713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6496 Z= 0.130 Angle : 0.616 10.608 9063 Z= 0.310 Chirality : 0.041 0.348 1042 Planarity : 0.004 0.048 959 Dihedral : 16.538 148.629 1519 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % 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 are not related in a simple way. whole: -1.28 (0.32), residues: 637 helix: 0.42 (0.44), residues: 152 sheet: -1.20 (0.55), residues: 75 loop : -1.32 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 205 TYR 0.009 0.001 TYR B 420 PHE 0.015 0.002 PHE B 350 TRP 0.038 0.002 TRP B 348 HIS 0.006 0.001 HIS B 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 ( 6479) covalent geometry : angle 0.61508 / 0.31 ( 9057) hydrogen bonds : bond 0.08989 / 6.80 ( 177) hydrogen bonds : angle 4.65927 / 3.23 ( 447) metal coordination : bond 0.00492 / 0.28 ( 16) metal coordination : angle 1.13336 / 0.62 ( 6) Misc. bond : bond 0.00104 / 0.05 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 57 MET cc_start: 0.8305 (mmm) cc_final: 0.7194 (mmm) REVERT: B 350 PHE cc_start: 0.7090 (m-80) cc_final: 0.6603 (m-10) REVERT: B 415 ASP cc_start: 0.7691 (m-30) cc_final: 0.7355 (m-30) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.0661 time to fit residues: 6.4760 Evaluate side-chains 65 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 30 optimal weight: 0.0870 chunk 0 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 47 optimal weight: 0.0010 chunk 14 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 17 optimal weight: 0.0000 chunk 52 optimal weight: 0.8980 overall best weight: 0.3970 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.050421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.039837 restraints weight = 36625.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.040904 restraints weight = 19543.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.041595 restraints weight = 12833.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.042054 restraints weight = 9735.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.042350 restraints weight = 8047.309| |-----------------------------------------------------------------------------| r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.4834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6496 Z= 0.106 Angle : 0.588 10.798 9063 Z= 0.294 Chirality : 0.040 0.334 1042 Planarity : 0.004 0.048 959 Dihedral : 16.477 152.121 1519 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % 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 are not related in a simple way. whole: -1.25 (0.33), residues: 637 helix: 0.47 (0.44), residues: 152 sheet: -1.31 (0.54), residues: 75 loop : -1.28 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 205 TYR 0.024 0.001 TYR B 260 PHE 0.017 0.001 PHE B 350 TRP 0.031 0.001 TRP B 348 HIS 0.003 0.001 HIS A 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 ( 6479) covalent geometry : angle 0.58735 / 0.29 ( 9057) hydrogen bonds : bond 0.08811 / 6.70 ( 177) hydrogen bonds : angle 4.55782 / 3.15 ( 447) metal coordination : bond 0.00369 / 0.24 ( 16) metal coordination : angle 1.13781 / 0.63 ( 6) Misc. bond : bond 0.00099 / 0.05 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1018.38 seconds wall clock time: 18 minutes 17.19 seconds (1097.19 seconds total)