Starting phenix.real_space_refine on Sat May 2 14:11:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vck_64956/05_2026/9vck_64956.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vck_64956/05_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_64956/05_2026/9vck_64956.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vck_64956/05_2026/9vck_64956.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vck_64956/05_2026/9vck_64956.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vck_64956/05_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-2.1rc2-6044/lib/python3.9/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: 1.66, per 1000 atoms: 0.27 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: 0.61 Conformation dependent library (CDL) restraints added in 328.2 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: 0.75 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: 1.11 Time building geometry restraints manager: 0.77 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 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: 2.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.000 Find NCS groups from input model: 0.030 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 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= 0.655 Angle : 1.147 29.223 9063 Z= 0.651 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 covalent geometry : bond 0.01021 ( 6479) covalent geometry : angle 1.09559 ( 9057) hydrogen bonds : bond 0.30553 ( 177) hydrogen bonds : angle 7.79047 ( 447) metal coordination : bond 0.18370 ( 16) metal coordination : angle 13.26123 ( 6) Misc. bond : bond 0.03232 ( 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 : 0.125 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: 0.1238 time to fit residues: 15.2620 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 : 0.247 ------------------------------------------------------------------------------- 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: 6.9990 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... Flipped N/Q/H residues before XYZ refinement: A 48 HIS A 53 GLN B 71 ASN B 245 GLN B 256 ASN ** B 486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.051497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.041133 restraints weight = 37322.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.042215 restraints weight = 19853.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.042938 restraints weight = 12822.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.043404 restraints weight = 9535.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.043677 restraints weight = 7809.796| |-----------------------------------------------------------------------------| r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2955 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= 0.145 Angle : 0.652 8.437 9063 Z= 0.333 Chirality : 0.042 0.187 1042 Planarity : 0.005 0.053 959 Dihedral : 17.302 117.411 1519 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.68 (0.30), residues: 637 helix: -0.88 (0.40), residues: 154 sheet: -2.33 (0.55), residues: 70 loop : -2.14 (0.28), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 78 TYR 0.018 0.002 TYR B 351 PHE 0.017 0.002 PHE A 68 TRP 0.020 0.002 TRP B 348 HIS 0.007 0.002 HIS A 48 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 6479) covalent geometry : angle 0.64969 ( 9057) hydrogen bonds : bond 0.09541 ( 177) hydrogen bonds : angle 4.96609 ( 447) metal coordination : bond 0.00755 ( 16) metal coordination : angle 2.40273 ( 6) Misc. bond : bond 0.00024 ( 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 97 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 PHE cc_start: 0.7782 (m-80) cc_final: 0.7319 (m-80) REVERT: B 285 CYS cc_start: 0.7838 (m) cc_final: 0.7607 (p) REVERT: B 350 PHE cc_start: 0.7083 (m-10) cc_final: 0.6230 (m-10) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.0968 time to fit residues: 12.0456 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 : 0.217 ------------------------------------------------------------------------------- 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: 0.7980 chunk 22 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 13 optimal weight: 0.0470 chunk 57 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 98 GLN B 245 GLN B 306 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.051026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.040450 restraints weight = 36094.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.041494 restraints weight = 19645.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.042188 restraints weight = 12963.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.042624 restraints weight = 9764.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.042851 restraints weight = 8122.219| |-----------------------------------------------------------------------------| r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6496 Z= 0.121 Angle : 0.598 11.843 9063 Z= 0.299 Chirality : 0.040 0.308 1042 Planarity : 0.004 0.048 959 Dihedral : 16.669 121.800 1519 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % 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: -2.09 (0.31), residues: 637 helix: -0.08 (0.42), residues: 150 sheet: -2.13 (0.53), residues: 75 loop : -1.83 (0.28), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 180 TYR 0.014 0.001 TYR B 351 PHE 0.019 0.002 PHE B 367 TRP 0.016 0.002 TRP B 348 HIS 0.003 0.001 HIS B 257 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 6479) covalent geometry : angle 0.59676 ( 9057) hydrogen bonds : bond 0.08251 ( 177) hydrogen bonds : angle 4.47555 ( 447) metal coordination : bond 0.00330 ( 16) metal coordination : angle 1.78327 ( 6) Misc. bond : bond 0.00139 ( 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 : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 GLN cc_start: 0.6044 (pt0) cc_final: 0.5810 (pm20) REVERT: A 82 ASP cc_start: 0.8361 (t0) cc_final: 0.8105 (t0) REVERT: B 18 LEU cc_start: 0.8181 (mm) cc_final: 0.7942 (mm) REVERT: B 57 MET cc_start: 0.8441 (mmm) cc_final: 0.7287 (mmm) REVERT: B 285 CYS cc_start: 0.7721 (m) cc_final: 0.7450 (p) REVERT: B 350 PHE cc_start: 0.6908 (m-10) cc_final: 0.6387 (m-10) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.1153 time to fit residues: 13.0606 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 : 0.213 ------------------------------------------------------------------------------- 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: 4.9990 chunk 8 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 16 optimal weight: 0.0050 chunk 3 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN ** B 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.050577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.040027 restraints weight = 36027.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.041081 restraints weight = 19345.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.041789 restraints weight = 12706.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.042241 restraints weight = 9535.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.042481 restraints weight = 7885.369| |-----------------------------------------------------------------------------| r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.4409 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 : 0.582 9.935 9063 Z= 0.291 Chirality : 0.040 0.204 1042 Planarity : 0.004 0.043 959 Dihedral : 16.530 134.382 1519 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.32), residues: 637 helix: 0.21 (0.43), residues: 151 sheet: -1.87 (0.54), residues: 75 loop : -1.68 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 205 TYR 0.013 0.001 TYR B 351 PHE 0.021 0.002 PHE A 68 TRP 0.015 0.001 TRP B 348 HIS 0.004 0.001 HIS A 83 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 6479) covalent geometry : angle 0.58125 ( 9057) hydrogen bonds : bond 0.08337 ( 177) hydrogen bonds : angle 4.45035 ( 447) metal coordination : bond 0.00397 ( 16) metal coordination : angle 1.47789 ( 6) Misc. bond : bond 0.00118 ( 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 89 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 ASP cc_start: 0.8428 (t0) cc_final: 0.8142 (t0) REVERT: A 85 ASN cc_start: 0.8357 (p0) cc_final: 0.7993 (p0) REVERT: B 57 MET cc_start: 0.8367 (mmm) cc_final: 0.7242 (mmm) REVERT: B 285 CYS cc_start: 0.7695 (m) cc_final: 0.7426 (p) REVERT: B 350 PHE cc_start: 0.7005 (m-10) cc_final: 0.5946 (m-10) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.1114 time to fit residues: 12.1343 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 : 0.210 ------------------------------------------------------------------------------- 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: 1.9990 chunk 13 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 67 optimal weight: 8.9990 chunk 62 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 46 optimal weight: 0.0770 chunk 12 optimal weight: 10.0000 chunk 35 optimal weight: 0.0980 overall best weight: 1.8344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN ** A 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 GLN B 354 GLN ** B 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.046763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.036213 restraints weight = 37276.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.037254 restraints weight = 19712.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.037912 restraints weight = 12855.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.038352 restraints weight = 9708.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.038585 restraints weight = 8080.692| |-----------------------------------------------------------------------------| r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.5070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 6496 Z= 0.234 Angle : 0.689 10.040 9063 Z= 0.354 Chirality : 0.043 0.182 1042 Planarity : 0.005 0.050 959 Dihedral : 17.025 148.694 1519 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 0.18 % Allowed : 4.15 % 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: -1.63 (0.32), residues: 637 helix: 0.19 (0.44), residues: 152 sheet: -1.29 (0.52), residues: 85 loop : -1.61 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 84 TYR 0.019 0.002 TYR A 96 PHE 0.019 0.002 PHE B 286 TRP 0.025 0.002 TRP B 348 HIS 0.006 0.001 HIS B 257 Details of bonding type rmsd covalent geometry : bond 0.00506 ( 6479) covalent geometry : angle 0.68688 ( 9057) hydrogen bonds : bond 0.08922 ( 177) hydrogen bonds : angle 5.07376 ( 447) metal coordination : bond 0.01067 ( 16) metal coordination : angle 2.06986 ( 6) Misc. bond : bond 0.00096 ( 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: 1 poor density : 85 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 ASP cc_start: 0.8416 (t0) cc_final: 0.8160 (t0) REVERT: A 85 ASN cc_start: 0.8464 (p0) cc_final: 0.7975 (p0) REVERT: B 57 MET cc_start: 0.8418 (mmm) cc_final: 0.7260 (mmm) REVERT: B 285 CYS cc_start: 0.7945 (m) cc_final: 0.7720 (p) REVERT: B 350 PHE cc_start: 0.7328 (m-10) cc_final: 0.6719 (m-10) REVERT: B 354 GLN cc_start: 0.7034 (OUTLIER) cc_final: 0.6783 (pp30) outliers start: 1 outliers final: 0 residues processed: 86 average time/residue: 0.0940 time to fit residues: 10.2686 Evaluate side-chains 67 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 66 time to evaluate : 0.202 ------------------------------------------------------------------------------- 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: 0.9980 chunk 20 optimal weight: 0.9980 chunk 10 optimal weight: 0.1980 chunk 26 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 48 optimal weight: 0.4980 chunk 54 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 HIS ** B 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.048431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.037877 restraints weight = 36791.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.038941 restraints weight = 19521.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.039634 restraints weight = 12645.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.040080 restraints weight = 9466.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.040372 restraints weight = 7863.992| |-----------------------------------------------------------------------------| r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.5393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 6496 Z= 0.122 Angle : 0.589 9.682 9063 Z= 0.294 Chirality : 0.041 0.363 1042 Planarity : 0.004 0.045 959 Dihedral : 16.753 160.284 1519 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % 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: 0.49 (0.44), residues: 152 sheet: -1.36 (0.53), residues: 81 loop : -1.48 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 205 TYR 0.008 0.001 TYR B 420 PHE 0.012 0.002 PHE A 89 TRP 0.025 0.002 TRP B 348 HIS 0.004 0.001 HIS B 486 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 6479) covalent geometry : angle 0.58792 ( 9057) hydrogen bonds : bond 0.08146 ( 177) hydrogen bonds : angle 4.65943 ( 447) metal coordination : bond 0.00329 ( 16) metal coordination : angle 1.29712 ( 6) Misc. bond : bond 0.00091 ( 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 : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 ASP cc_start: 0.8373 (t0) cc_final: 0.8106 (t0) REVERT: A 85 ASN cc_start: 0.8488 (p0) cc_final: 0.8072 (p0) REVERT: B 57 MET cc_start: 0.8257 (mmm) cc_final: 0.7379 (mmm) REVERT: B 285 CYS cc_start: 0.7509 (m) cc_final: 0.7277 (p) REVERT: B 401 PHE cc_start: 0.8569 (t80) cc_final: 0.8279 (t80) REVERT: B 415 ASP cc_start: 0.7375 (m-30) cc_final: 0.7045 (m-30) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.0929 time to fit residues: 9.9869 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: 0.0670 chunk 57 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 64 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 11 optimal weight: 0.1980 chunk 67 optimal weight: 8.9990 chunk 29 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.0122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 GLN ** B 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.047874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.037348 restraints weight = 36997.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.038399 restraints weight = 19657.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.039085 restraints weight = 12826.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.039531 restraints weight = 9621.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.039761 restraints weight = 7987.069| |-----------------------------------------------------------------------------| r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.5683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6496 Z= 0.146 Angle : 0.593 8.997 9063 Z= 0.301 Chirality : 0.041 0.300 1042 Planarity : 0.004 0.045 959 Dihedral : 16.690 168.772 1519 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % 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: -1.32 (0.33), residues: 637 helix: 0.39 (0.44), residues: 152 sheet: -1.09 (0.52), residues: 89 loop : -1.37 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 84 TYR 0.008 0.001 TYR B 235 PHE 0.018 0.002 PHE B 367 TRP 0.026 0.002 TRP B 348 HIS 0.004 0.001 HIS A 83 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 6479) covalent geometry : angle 0.59234 ( 9057) hydrogen bonds : bond 0.08114 ( 177) hydrogen bonds : angle 4.76005 ( 447) metal coordination : bond 0.00426 ( 16) metal coordination : angle 1.03796 ( 6) Misc. bond : bond 0.00071 ( 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 82 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 ASN cc_start: 0.8468 (p0) cc_final: 0.8091 (p0) REVERT: A 106 ASP cc_start: 0.8298 (t0) cc_final: 0.7897 (t0) REVERT: B 49 MET cc_start: 0.8397 (ppp) cc_final: 0.8181 (ppp) REVERT: B 57 MET cc_start: 0.8154 (mmm) cc_final: 0.7238 (mmm) REVERT: B 285 CYS cc_start: 0.7681 (m) cc_final: 0.7386 (p) REVERT: B 415 ASP cc_start: 0.7708 (m-30) cc_final: 0.7369 (m-30) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.0931 time to fit residues: 9.8641 Evaluate side-chains 67 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.215 ------------------------------------------------------------------------------- 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: 3.9990 chunk 7 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 2 optimal weight: 0.0370 chunk 24 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 GLN ** B 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.048413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.038001 restraints weight = 37259.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.039025 restraints weight = 20256.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.039679 restraints weight = 13401.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.040114 restraints weight = 10177.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.040344 restraints weight = 8498.350| |-----------------------------------------------------------------------------| r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.5884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6496 Z= 0.120 Angle : 0.577 8.933 9063 Z= 0.288 Chirality : 0.040 0.254 1042 Planarity : 0.004 0.044 959 Dihedral : 16.553 173.339 1519 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % 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: -1.16 (0.33), residues: 637 helix: 0.58 (0.45), residues: 152 sheet: -1.04 (0.54), residues: 83 loop : -1.28 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 205 TYR 0.017 0.001 TYR B 351 PHE 0.009 0.001 PHE B 286 TRP 0.029 0.002 TRP B 348 HIS 0.004 0.001 HIS B 268 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 6479) covalent geometry : angle 0.57644 ( 9057) hydrogen bonds : bond 0.07902 ( 177) hydrogen bonds : angle 4.65406 ( 447) metal coordination : bond 0.00264 ( 16) metal coordination : angle 0.96437 ( 6) Misc. bond : bond 0.00068 ( 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 83 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 LYS cc_start: 0.8978 (mmmt) cc_final: 0.8705 (mmmm) REVERT: A 85 ASN cc_start: 0.8392 (p0) cc_final: 0.8023 (p0) REVERT: A 106 ASP cc_start: 0.8253 (t0) cc_final: 0.7920 (t0) REVERT: B 57 MET cc_start: 0.8196 (mmm) cc_final: 0.7336 (mmm) REVERT: B 285 CYS cc_start: 0.7612 (m) cc_final: 0.7362 (p) REVERT: B 350 PHE cc_start: 0.6993 (m-10) cc_final: 0.6602 (m-10) REVERT: B 415 ASP cc_start: 0.7398 (m-30) cc_final: 0.7083 (m-30) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.0978 time to fit residues: 10.3135 Evaluate side-chains 71 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.203 ------------------------------------------------------------------------------- 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: 1.9990 chunk 54 optimal weight: 3.9990 chunk 2 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 HIS ** B 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 GLN B 268 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.048139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.037727 restraints weight = 36608.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.038752 restraints weight = 19868.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.039421 restraints weight = 12992.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.039853 restraints weight = 9774.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.040147 restraints weight = 8112.486| |-----------------------------------------------------------------------------| r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.6042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6496 Z= 0.123 Angle : 0.585 8.906 9063 Z= 0.294 Chirality : 0.040 0.237 1042 Planarity : 0.004 0.042 959 Dihedral : 16.489 174.792 1519 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % 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: -1.07 (0.33), residues: 637 helix: 0.53 (0.44), residues: 152 sheet: -0.99 (0.54), residues: 83 loop : -1.17 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 205 TYR 0.006 0.001 TYR A 30 PHE 0.020 0.002 PHE B 367 TRP 0.030 0.002 TRP B 348 HIS 0.004 0.001 HIS A 83 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 6479) covalent geometry : angle 0.58416 ( 9057) hydrogen bonds : bond 0.07873 ( 177) hydrogen bonds : angle 4.65459 ( 447) metal coordination : bond 0.00257 ( 16) metal coordination : angle 0.97527 ( 6) Misc. bond : bond 0.00060 ( 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 : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 LYS cc_start: 0.8668 (mmmt) cc_final: 0.8383 (tppt) REVERT: A 106 ASP cc_start: 0.8304 (t0) cc_final: 0.7889 (t0) REVERT: B 57 MET cc_start: 0.8166 (mmm) cc_final: 0.7320 (mmm) REVERT: B 284 GLU cc_start: 0.8540 (mm-30) cc_final: 0.7971 (mm-30) REVERT: B 285 CYS cc_start: 0.7664 (m) cc_final: 0.7415 (p) REVERT: B 350 PHE cc_start: 0.7014 (m-10) cc_final: 0.6729 (m-10) REVERT: B 415 ASP cc_start: 0.7449 (m-30) cc_final: 0.7197 (m-30) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.0812 time to fit residues: 8.6157 Evaluate side-chains 71 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.202 ------------------------------------------------------------------------------- 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: 3.9990 chunk 37 optimal weight: 2.9990 chunk 67 optimal weight: 8.9990 chunk 18 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN B 108 GLN ** B 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 GLN B 422 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.046531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.036242 restraints weight = 36620.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.037250 restraints weight = 19788.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.037888 restraints weight = 13063.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.038286 restraints weight = 9920.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.038564 restraints weight = 8280.423| |-----------------------------------------------------------------------------| r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.6255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6496 Z= 0.178 Angle : 0.640 12.387 9063 Z= 0.321 Chirality : 0.042 0.236 1042 Planarity : 0.005 0.044 959 Dihedral : 16.631 176.959 1519 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % 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: -1.11 (0.33), residues: 637 helix: 0.45 (0.44), residues: 152 sheet: -0.74 (0.55), residues: 87 loop : -1.25 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 84 TYR 0.014 0.002 TYR B 351 PHE 0.017 0.002 PHE B 286 TRP 0.030 0.002 TRP B 348 HIS 0.004 0.001 HIS B 373 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 6479) covalent geometry : angle 0.63835 ( 9057) hydrogen bonds : bond 0.08236 ( 177) hydrogen bonds : angle 4.96810 ( 447) metal coordination : bond 0.00858 ( 16) metal coordination : angle 1.62873 ( 6) Misc. bond : bond 0.00054 ( 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 78 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.8370 (t0) cc_final: 0.8127 (t0) REVERT: B 57 MET cc_start: 0.8214 (mmm) cc_final: 0.7338 (mmm) REVERT: B 246 GLN cc_start: 0.8543 (mp10) cc_final: 0.8198 (mp10) REVERT: B 284 GLU cc_start: 0.8605 (mm-30) cc_final: 0.8075 (mm-30) REVERT: B 367 PHE cc_start: 0.7798 (t80) cc_final: 0.7503 (t80) REVERT: B 415 ASP cc_start: 0.7758 (m-30) cc_final: 0.7462 (m-30) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.0887 time to fit residues: 8.8958 Evaluate side-chains 67 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.174 ------------------------------------------------------------------------------- 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: 0.1980 chunk 0 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 58 optimal weight: 0.0370 chunk 17 optimal weight: 0.0770 chunk 52 optimal weight: 0.0270 overall best weight: 0.2074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 GLN B 245 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.049364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.039030 restraints weight = 36638.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.040066 restraints weight = 19811.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.040747 restraints weight = 13050.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.041204 restraints weight = 9806.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.041491 restraints weight = 8052.566| |-----------------------------------------------------------------------------| r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.6473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6496 Z= 0.100 Angle : 0.577 8.822 9063 Z= 0.286 Chirality : 0.039 0.210 1042 Planarity : 0.004 0.042 959 Dihedral : 16.344 179.814 1519 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % 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: -0.99 (0.33), residues: 637 helix: 0.54 (0.43), residues: 152 sheet: -1.00 (0.55), residues: 83 loop : -1.07 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 404 TYR 0.006 0.001 TYR B 420 PHE 0.009 0.001 PHE B 350 TRP 0.032 0.002 TRP B 348 HIS 0.004 0.001 HIS B 268 Details of bonding type rmsd covalent geometry : bond 0.00216 ( 6479) covalent geometry : angle 0.57676 ( 9057) hydrogen bonds : bond 0.07813 ( 177) hydrogen bonds : angle 4.56911 ( 447) metal coordination : bond 0.00445 ( 16) metal coordination : angle 1.11846 ( 6) Misc. bond : bond 0.00104 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1193.38 seconds wall clock time: 21 minutes 23.89 seconds (1283.89 seconds total)