Starting phenix.real_space_refine on Thu Jul 2 03:35:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vck_64956/07_2026/9vck_64956.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vck_64956/07_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_64956/07_2026/9vck_64956.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vck_64956/07_2026/9vck_64956.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vck_64956/07_2026/9vck_64956.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vck_64956/07_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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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, 3 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain breaks: 2 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: 1.26, per 1000 atoms: 0.20 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: 0.40 Conformation dependent library (CDL) restraints added in 212.4 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: 0.63 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: 1.01 Time building geometry restraints manager: 0.49 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: 9026 5.84 - 11.69: 22 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 1.50e+00 4.44e-01 1.39e+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 3.250 nonbonded pdb=" OD2 ASP B 90 " pdb="CA CA B 601 " model vdw 1.918 3.250 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: 2.950 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.820 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:0.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.800 ------------------------------------------------------------------------------- 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= 0.664 Angle : 1.147 29.223 9063 Z= 0.666 Chirality : 0.074 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 0.01021 / 0.59 ( 6479) covalent geometry : angle 1.09559 / 0.66 ( 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 : 0.128 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: 0.0942 time to fit residues: 11.8112 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 : 0.159 ------------------------------------------------------------------------------- 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: 10.0000 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 = 0.3224 r_free = 0.3224 target = 0.052249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.041963 restraints weight = 38244.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.043049 restraints weight = 20258.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.043757 restraints weight = 13088.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.044233 restraints weight = 9694.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.044482 restraints weight = 7915.288| |-----------------------------------------------------------------------------| r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6496 Z= 0.173 Angle : 0.711 10.709 9063 Z= 0.376 Chirality : 0.045 0.212 1042 Planarity : 0.006 0.064 959 Dihedral : 17.728 109.169 1519 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 0.18 % Allowed : 7.04 % Favored : 92.78 % 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: -2.80 (0.30), residues: 637 helix: -1.25 (0.39), residues: 153 sheet: -2.18 (0.58), residues: 65 loop : -2.16 (0.28), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 476 TYR 0.025 0.002 TYR B 351 PHE 0.029 0.002 PHE A 68 TRP 0.020 0.002 TRP B 348 HIS 0.009 0.002 HIS B 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.17 ( 6479) covalent geometry : angle 0.70797 / 0.38 ( 9057) hydrogen bonds : bond 0.10078 / 7.55 ( 177) hydrogen bonds : angle 5.42570 / 3.76 ( 447) metal coordination : bond 0.00707 / 0.49 ( 16) metal coordination : angle 2.79231 / 1.47 ( 6) Misc. bond : bond 0.00412 / 0.20 ( 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 : 0.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 PHE cc_start: 0.7867 (m-80) cc_final: 0.7517 (m-80) REVERT: B 72 MET cc_start: 0.8881 (mtm) cc_final: 0.8664 (mtm) REVERT: B 115 VAL cc_start: 0.8902 (t) cc_final: 0.8668 (t) outliers start: 1 outliers final: 0 residues processed: 90 average time/residue: 0.0752 time to fit residues: 8.6318 Evaluate side-chains 69 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.135 ------------------------------------------------------------------------------- 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: 1.9990 chunk 42 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3201 r_free = 0.3201 target = 0.051631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.041189 restraints weight = 37165.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.042250 restraints weight = 20180.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.042936 restraints weight = 13304.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.043366 restraints weight = 10068.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.043684 restraints weight = 8338.985| |-----------------------------------------------------------------------------| r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2898 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= 0.150 Angle : 0.635 9.501 9063 Z= 0.333 Chirality : 0.042 0.181 1042 Planarity : 0.005 0.052 959 Dihedral : 17.430 110.522 1519 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % 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: -0.70 (0.40), residues: 154 sheet: -2.14 (0.58), residues: 65 loop : -1.91 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 180 TYR 0.026 0.002 TYR B 351 PHE 0.019 0.002 PHE B 367 TRP 0.024 0.002 TRP B 348 HIS 0.005 0.002 HIS B 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 ( 6479) covalent geometry : angle 0.63215 / 0.33 ( 9057) hydrogen bonds : bond 0.10162 / 7.69 ( 177) hydrogen bonds : angle 4.96686 / 3.44 ( 447) metal coordination : bond 0.00336 / 0.22 ( 16) metal coordination : angle 2.32869 / 1.26 ( 6) Misc. bond : bond 0.00087 / 0.04 ( 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 92 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8447 (tpp) cc_final: 0.8193 (tpp) REVERT: A 68 PHE cc_start: 0.7906 (m-80) cc_final: 0.7617 (m-80) REVERT: B 57 MET cc_start: 0.8410 (mmm) cc_final: 0.7186 (mmm) REVERT: B 350 PHE cc_start: 0.7126 (m-10) cc_final: 0.6500 (m-10) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.0738 time to fit residues: 8.7392 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 : 0.149 ------------------------------------------------------------------------------- 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: 0.6980 chunk 8 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 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: 0.9990 chunk 30 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 37 optimal weight: 0.0670 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.051527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.040957 restraints weight = 36883.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.042023 restraints weight = 19867.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.042723 restraints weight = 13031.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.043181 restraints weight = 9791.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.043455 restraints weight = 8116.134| |-----------------------------------------------------------------------------| r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6496 Z= 0.132 Angle : 0.608 10.358 9063 Z= 0.318 Chirality : 0.042 0.329 1042 Planarity : 0.005 0.056 959 Dihedral : 17.082 114.108 1519 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % 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: -2.19 (0.31), residues: 637 helix: -0.33 (0.41), residues: 153 sheet: -2.26 (0.53), residues: 75 loop : -1.82 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 84 TYR 0.017 0.001 TYR B 420 PHE 0.016 0.001 PHE A 89 TRP 0.024 0.002 TRP B 348 HIS 0.003 0.001 HIS B 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 6479) covalent geometry : angle 0.60643 / 0.32 ( 9057) hydrogen bonds : bond 0.09355 / 7.16 ( 177) hydrogen bonds : angle 4.80917 / 3.32 ( 447) metal coordination : bond 0.00402 / 0.22 ( 16) metal coordination : angle 1.84351 / 1.05 ( 6) Misc. bond : bond 0.00073 / 0.03 ( 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 88 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 PHE cc_start: 0.7804 (m-80) cc_final: 0.7155 (m-80) REVERT: A 82 ASP cc_start: 0.8326 (t0) cc_final: 0.8063 (t0) REVERT: B 350 PHE cc_start: 0.7282 (m-10) cc_final: 0.6163 (m-10) REVERT: B 415 ASP cc_start: 0.7469 (m-30) cc_final: 0.7222 (m-30) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.0730 time to fit residues: 8.2115 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 : 0.124 ------------------------------------------------------------------------------- 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: 0.7980 chunk 13 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 11 optimal weight: 0.4980 chunk 67 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 35 optimal weight: 0.1980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 486 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.051176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.040488 restraints weight = 36753.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.041572 restraints weight = 19667.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.042296 restraints weight = 12836.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.042724 restraints weight = 9617.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.043052 restraints weight = 7987.747| |-----------------------------------------------------------------------------| r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6496 Z= 0.128 Angle : 0.611 8.293 9063 Z= 0.317 Chirality : 0.041 0.243 1042 Planarity : 0.005 0.050 959 Dihedral : 16.907 116.970 1519 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % 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: -1.91 (0.32), residues: 637 helix: 0.09 (0.43), residues: 151 sheet: -2.14 (0.52), residues: 75 loop : -1.69 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 78 TYR 0.013 0.001 TYR B 420 PHE 0.038 0.002 PHE A 68 TRP 0.022 0.002 TRP B 348 HIS 0.008 0.001 HIS B 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 ( 6479) covalent geometry : angle 0.61047 / 0.32 ( 9057) hydrogen bonds : bond 0.09276 / 7.08 ( 177) hydrogen bonds : angle 4.75663 / 3.28 ( 447) metal coordination : bond 0.00270 / 0.15 ( 16) metal coordination : angle 1.29410 / 0.70 ( 6) Misc. bond : bond 0.00026 / 0.01 ( 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 84 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.202 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: 0.7134 (m-80) cc_final: 0.6815 (m-80) REVERT: A 82 ASP cc_start: 0.8360 (t0) cc_final: 0.8093 (t0) REVERT: B 57 MET cc_start: 0.8336 (mmm) cc_final: 0.7196 (mmm) REVERT: B 350 PHE cc_start: 0.7182 (m-10) cc_final: 0.6374 (m-10) REVERT: B 415 ASP cc_start: 0.7683 (m-30) cc_final: 0.7298 (m-30) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.0755 time to fit residues: 8.1684 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 : 0.146 ------------------------------------------------------------------------------- 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: 6.9990 chunk 11 optimal weight: 0.0970 chunk 20 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 48 optimal weight: 0.4980 chunk 54 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 65 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.051060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.040419 restraints weight = 36938.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.041517 restraints weight = 19733.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.042245 restraints weight = 12855.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.042730 restraints weight = 9640.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.042988 restraints weight = 7895.987| |-----------------------------------------------------------------------------| r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.3916 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= 0.121 Angle : 0.596 11.722 9063 Z= 0.306 Chirality : 0.040 0.192 1042 Planarity : 0.004 0.048 959 Dihedral : 16.744 118.635 1519 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 11.41 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: -1.86 (0.32), residues: 637 helix: 0.12 (0.42), residues: 151 sheet: -2.00 (0.53), residues: 77 loop : -1.67 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 212 TYR 0.012 0.001 TYR B 420 PHE 0.023 0.001 PHE B 350 TRP 0.025 0.002 TRP B 348 HIS 0.003 0.001 HIS B 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 ( 6479) covalent geometry : angle 0.59492 / 0.31 ( 9057) hydrogen bonds : bond 0.09123 / 6.97 ( 177) hydrogen bonds : angle 4.69343 / 3.24 ( 447) metal coordination : bond 0.00879 / 0.65 ( 16) metal coordination : angle 1.21248 / 0.66 ( 6) Misc. bond : bond 0.00121 / 0.06 ( 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 81 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 PHE cc_start: 0.7517 (m-80) cc_final: 0.7309 (m-80) REVERT: A 82 ASP cc_start: 0.8392 (t0) cc_final: 0.8075 (t0) REVERT: B 57 MET cc_start: 0.8352 (mmm) cc_final: 0.7132 (mmm) REVERT: B 350 PHE cc_start: 0.7049 (m-80) cc_final: 0.6352 (m-10) REVERT: B 415 ASP cc_start: 0.7650 (m-30) cc_final: 0.7285 (m-30) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.0795 time to fit residues: 8.2722 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 : 0.166 ------------------------------------------------------------------------------- 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: 0.6980 chunk 64 optimal weight: 10.0000 chunk 56 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 67 optimal weight: 10.0000 chunk 29 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 GLN ** B 424 HIS ** 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 = 0.3118 r_free = 0.3118 target = 0.048892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.038239 restraints weight = 36646.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.039329 restraints weight = 19664.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.040038 restraints weight = 12844.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.040436 restraints weight = 9650.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.040784 restraints weight = 8047.894| |-----------------------------------------------------------------------------| r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.4272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6496 Z= 0.177 Angle : 0.635 10.289 9063 Z= 0.329 Chirality : 0.042 0.200 1042 Planarity : 0.005 0.050 959 Dihedral : 16.586 119.840 1519 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % 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: -1.59 (0.32), residues: 637 helix: 0.36 (0.44), residues: 151 sheet: -1.58 (0.51), residues: 81 loop : -1.56 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 53 TYR 0.025 0.002 TYR B 447 PHE 0.022 0.002 PHE B 350 TRP 0.030 0.002 TRP B 348 HIS 0.012 0.002 HIS B 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.18 ( 6479) covalent geometry : angle 0.63113 / 0.33 ( 9057) hydrogen bonds : bond 0.09283 / 6.96 ( 177) hydrogen bonds : angle 4.83175 / 3.33 ( 447) metal coordination : bond 0.01058 / 0.66 ( 16) metal coordination : angle 2.95251 / 1.36 ( 6) Misc. bond : bond 0.00052 / 0.02 ( 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 : 0.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 MET cc_start: 0.8187 (pmm) cc_final: 0.7870 (pmm) REVERT: A 82 ASP cc_start: 0.8404 (t0) cc_final: 0.8121 (t0) REVERT: B 57 MET cc_start: 0.8355 (mmm) cc_final: 0.7193 (mmm) REVERT: B 350 PHE cc_start: 0.7307 (m-80) cc_final: 0.6664 (m-10) REVERT: B 415 ASP cc_start: 0.7794 (m-30) cc_final: 0.7427 (m-30) REVERT: B 433 LYS cc_start: 0.9266 (pptt) cc_final: 0.9047 (pptt) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.0739 time to fit residues: 7.6681 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 : 0.148 ------------------------------------------------------------------------------- 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: 0.4980 chunk 7 optimal weight: 0.9990 chunk 12 optimal weight: 0.0670 chunk 30 optimal weight: 2.9990 chunk 37 optimal weight: 0.2980 chunk 2 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.4920 ------------------------------------------------------------------------------- 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 = 0.3154 r_free = 0.3154 target = 0.049966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.039300 restraints weight = 36994.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.040393 restraints weight = 19610.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.041115 restraints weight = 12774.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.041596 restraints weight = 9534.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.041833 restraints weight = 7900.832| |-----------------------------------------------------------------------------| r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.4471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6496 Z= 0.113 Angle : 0.595 9.933 9063 Z= 0.304 Chirality : 0.041 0.386 1042 Planarity : 0.004 0.049 959 Dihedral : 16.440 120.003 1519 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % 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: -1.52 (0.32), residues: 637 helix: 0.44 (0.44), residues: 151 sheet: -1.50 (0.54), residues: 75 loop : -1.55 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 400 TYR 0.011 0.001 TYR B 420 PHE 0.016 0.001 PHE B 350 TRP 0.029 0.002 TRP B 348 HIS 0.006 0.001 HIS B 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 ( 6479) covalent geometry : angle 0.59476 / 0.30 ( 9057) hydrogen bonds : bond 0.08911 / 6.79 ( 177) hydrogen bonds : angle 4.68329 / 3.24 ( 447) metal coordination : bond 0.00447 / 0.26 ( 16) metal coordination : angle 1.28584 / 0.70 ( 6) Misc. bond : bond 0.00098 / 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 79 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 MET cc_start: 0.8195 (pmm) cc_final: 0.7856 (pmm) REVERT: A 68 PHE cc_start: 0.7439 (m-80) cc_final: 0.6331 (m-80) REVERT: A 82 ASP cc_start: 0.8357 (t0) cc_final: 0.8047 (t0) REVERT: B 49 MET cc_start: 0.8132 (ppp) cc_final: 0.7862 (ppp) REVERT: B 57 MET cc_start: 0.8321 (mmm) cc_final: 0.7193 (mmm) REVERT: B 350 PHE cc_start: 0.7239 (m-80) cc_final: 0.6786 (m-10) REVERT: B 415 ASP cc_start: 0.7703 (m-30) cc_final: 0.7375 (m-30) REVERT: B 433 LYS cc_start: 0.9285 (pptt) cc_final: 0.9070 (pptt) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.0761 time to fit residues: 7.7165 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 : 0.147 ------------------------------------------------------------------------------- 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: 0.6980 chunk 23 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 19 optimal weight: 0.0770 chunk 60 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 42 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 overall best weight: 0.6338 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.050026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.039397 restraints weight = 36745.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.040470 restraints weight = 19586.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.041193 restraints weight = 12700.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.041664 restraints weight = 9498.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.041998 restraints weight = 7812.808| |-----------------------------------------------------------------------------| r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.4637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6496 Z= 0.119 Angle : 0.589 11.335 9063 Z= 0.298 Chirality : 0.041 0.383 1042 Planarity : 0.005 0.047 959 Dihedral : 16.263 120.629 1519 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % 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: -1.41 (0.32), residues: 637 helix: 0.45 (0.44), residues: 151 sheet: -1.32 (0.54), residues: 75 loop : -1.46 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 84 TYR 0.010 0.001 TYR B 351 PHE 0.024 0.002 PHE B 367 TRP 0.032 0.002 TRP B 348 HIS 0.005 0.001 HIS B 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 ( 6479) covalent geometry : angle 0.58822 / 0.30 ( 9057) hydrogen bonds : bond 0.08842 / 6.72 ( 177) hydrogen bonds : angle 4.65565 / 3.21 ( 447) metal coordination : bond 0.00248 / 0.16 ( 16) metal coordination : angle 1.13762 / 0.62 ( 6) Misc. bond : bond 0.00089 / 0.04 ( 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 81 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 MET cc_start: 0.8110 (pmm) cc_final: 0.7739 (pmm) REVERT: A 65 GLN cc_start: 0.6264 (pt0) cc_final: 0.5999 (pm20) REVERT: A 82 ASP cc_start: 0.8377 (t0) cc_final: 0.8100 (t0) REVERT: B 49 MET cc_start: 0.8152 (ppp) cc_final: 0.7848 (ppp) REVERT: B 57 MET cc_start: 0.8336 (mmm) cc_final: 0.7221 (mmm) REVERT: B 350 PHE cc_start: 0.7246 (m-80) cc_final: 0.6842 (m-10) REVERT: B 415 ASP cc_start: 0.7710 (m-30) cc_final: 0.7366 (m-30) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.0862 time to fit residues: 8.9543 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 : 0.145 ------------------------------------------------------------------------------- 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: 0.0770 chunk 37 optimal weight: 0.5980 chunk 67 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 42 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.049902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.039328 restraints weight = 36866.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.040436 restraints weight = 19446.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.041175 restraints weight = 12634.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.041643 restraints weight = 9432.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.041924 restraints weight = 7772.626| |-----------------------------------------------------------------------------| r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.4835 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= 0.119 Angle : 0.594 10.870 9063 Z= 0.301 Chirality : 0.041 0.342 1042 Planarity : 0.005 0.048 959 Dihedral : 16.171 121.160 1519 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % 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: -1.30 (0.32), residues: 637 helix: 0.48 (0.44), residues: 151 sheet: -1.31 (0.55), residues: 75 loop : -1.35 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 205 TYR 0.023 0.001 TYR B 260 PHE 0.035 0.002 PHE B 350 TRP 0.028 0.002 TRP B 348 HIS 0.004 0.001 HIS B 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 ( 6479) covalent geometry : angle 0.59380 / 0.30 ( 9057) hydrogen bonds : bond 0.08706 / 6.63 ( 177) hydrogen bonds : angle 4.58351 / 3.17 ( 447) metal coordination : bond 0.00262 / 0.15 ( 16) metal coordination : angle 1.00893 / 0.54 ( 6) Misc. bond : bond 0.00079 / 0.04 ( 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 81 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 MET cc_start: 0.8104 (pmm) cc_final: 0.7742 (pmm) REVERT: A 64 ASP cc_start: 0.7138 (t0) cc_final: 0.6927 (t0) REVERT: A 82 ASP cc_start: 0.8353 (t0) cc_final: 0.8078 (t0) REVERT: B 49 MET cc_start: 0.8149 (ppp) cc_final: 0.7833 (ppp) REVERT: B 57 MET cc_start: 0.8319 (mmm) cc_final: 0.7176 (mmm) REVERT: B 415 ASP cc_start: 0.7687 (m-30) cc_final: 0.7369 (m-30) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.0698 time to fit residues: 7.3131 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 : 0.124 ------------------------------------------------------------------------------- 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: 1.9990 chunk 0 optimal weight: 6.9990 chunk 38 optimal weight: 0.4980 chunk 53 optimal weight: 1.9990 chunk 50 optimal weight: 0.4980 chunk 43 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 17 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 GLN B 486 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.049905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.039213 restraints weight = 36655.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.040304 restraints weight = 19442.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.041040 restraints weight = 12673.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.041526 restraints weight = 9499.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.041770 restraints weight = 7812.390| |-----------------------------------------------------------------------------| r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.4909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6496 Z= 0.118 Angle : 0.589 10.757 9063 Z= 0.298 Chirality : 0.041 0.326 1042 Planarity : 0.005 0.047 959 Dihedral : 16.109 121.478 1519 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % 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: -1.26 (0.33), residues: 637 helix: 0.43 (0.44), residues: 151 sheet: -1.38 (0.55), residues: 75 loop : -1.26 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 205 TYR 0.008 0.001 TYR B 420 PHE 0.032 0.002 PHE B 350 TRP 0.025 0.002 TRP B 348 HIS 0.004 0.001 HIS B 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 ( 6479) covalent geometry : angle 0.58853 / 0.30 ( 9057) hydrogen bonds : bond 0.08649 / 6.57 ( 177) hydrogen bonds : angle 4.56452 / 3.16 ( 447) metal coordination : bond 0.00224 / 0.13 ( 16) metal coordination : angle 0.99811 / 0.55 ( 6) Misc. bond : bond 0.00077 / 0.04 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 951.70 seconds wall clock time: 17 minutes 16.04 seconds (1036.04 seconds total)