Starting phenix.real_space_refine on Wed Mar 12 13:40:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ifk_35419/03_2025/8ifk_35419.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ifk_35419/03_2025/8ifk_35419.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ifk_35419/03_2025/8ifk_35419.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ifk_35419/03_2025/8ifk_35419.map" model { file = "/net/cci-nas-00/data/ceres_data/8ifk_35419/03_2025/8ifk_35419.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ifk_35419/03_2025/8ifk_35419.cif" } resolution = 2.54 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.227 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: 6 Type Number sf(0) Gaussians P 41 5.49 5 Mg 1 5.21 5 S 21 5.16 5 C 4808 2.51 5 N 1280 2.21 5 O 1481 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 7632 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3475 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 14, 'TRANS': 399} Chain breaks: 2 Chain: "B" Number of atoms: 3300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3300 Classifications: {'peptide': 409} Link IDs: {'PTRANS': 24, 'TRANS': 384} Chain breaks: 6 Chain: "C" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 423 Classifications: {'RNA': 20} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 8, 'rna3p_pyr': 10} Link IDs: {'rna2p': 1, 'rna3p': 18} Chain: "D" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 433 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.67, per 1000 atoms: 0.74 Number of scatterers: 7632 At special positions: 0 Unit cell: (75.9, 86.9, 129.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 21 16.00 P 41 15.00 Mg 1 11.99 O 1481 8.00 N 1280 7.00 C 4808 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=0, symmetry=0 Time building additional restraints: 2.15 Conformation dependent library (CDL) restraints added in 780.9 milliseconds 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1566 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 9 sheets defined 38.5% alpha, 17.9% beta 17 base pairs and 30 stacking pairs defined. Time for finding SS restraints: 3.11 Creating SS restraints... Processing helix chain 'A' and resid 14 through 28 Processing helix chain 'A' and resid 34 through 38 removed outlier: 3.908A pdb=" N PHE A 38 " --> pdb=" O ASP A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 55 Processing helix chain 'A' and resid 65 through 70 removed outlier: 4.428A pdb=" N LYS A 70 " --> pdb=" O THR A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 89 Processing helix chain 'A' and resid 109 through 114 removed outlier: 4.034A pdb=" N ARG A 114 " --> pdb=" O ILE A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 138 Processing helix chain 'A' and resid 146 through 158 removed outlier: 3.665A pdb=" N SER A 150 " --> pdb=" O ASP A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 203 Processing helix chain 'A' and resid 227 through 231 removed outlier: 3.698A pdb=" N GLU A 231 " --> pdb=" O PRO A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 238 removed outlier: 3.851A pdb=" N GLU A 237 " --> pdb=" O ASN A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 248 Processing helix chain 'A' and resid 257 through 279 removed outlier: 3.564A pdb=" N LYS A 278 " --> pdb=" O GLU A 274 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASP A 279 " --> pdb=" O LEU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 302 No H-bonds generated for 'chain 'A' and resid 300 through 302' Processing helix chain 'A' and resid 353 through 366 Processing helix chain 'A' and resid 369 through 384 Processing helix chain 'B' and resid 15 through 17 No H-bonds generated for 'chain 'B' and resid 15 through 17' Processing helix chain 'B' and resid 22 through 30 Processing helix chain 'B' and resid 46 through 62 removed outlier: 3.676A pdb=" N LYS B 62 " --> pdb=" O ASP B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 83 Processing helix chain 'B' and resid 87 through 89 No H-bonds generated for 'chain 'B' and resid 87 through 89' Processing helix chain 'B' and resid 115 through 129 removed outlier: 4.215A pdb=" N ALA B 128 " --> pdb=" O LYS B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 214 Processing helix chain 'B' and resid 226 through 230 Processing helix chain 'B' and resid 248 through 264 Processing helix chain 'B' and resid 331 through 351 Processing helix chain 'B' and resid 366 through 375 Processing helix chain 'B' and resid 451 through 463 Processing helix chain 'B' and resid 477 through 491 Processing helix chain 'B' and resid 502 through 506 Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 33 removed outlier: 5.924A pdb=" N ILE A 5 " --> pdb=" O TRP A 33 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LYS A 4 " --> pdb=" O LYS A 59 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N LEU A 61 " --> pdb=" O LYS A 4 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N PHE A 6 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N VAL A 63 " --> pdb=" O PHE A 6 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N SER A 8 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 8.406A pdb=" N ILE A 95 " --> pdb=" O CYS A 58 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N PHE A 60 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N LEU A 97 " --> pdb=" O PHE A 60 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILE A 62 " --> pdb=" O LEU A 97 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 319 through 324 removed outlier: 4.340A pdb=" N TYR B 280 " --> pdb=" O MET B 303 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N CYS B 279 " --> pdb=" O PHE B 358 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N HIS B 360 " --> pdb=" O CYS B 279 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N LEU B 281 " --> pdb=" O HIS B 360 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL B 357 " --> pdb=" O VAL B 384 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N VAL B 386 " --> pdb=" O VAL B 357 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ILE B 359 " --> pdb=" O VAL B 386 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ILE B 388 " --> pdb=" O ILE B 359 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N ALA B 361 " --> pdb=" O ILE B 388 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N THR B 387 " --> pdb=" O ILE B 445 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N ILE B 445 " --> pdb=" O THR B 387 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N THR B 389 " --> pdb=" O ILE B 443 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ILE B 443 " --> pdb=" O THR B 389 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LYS A 409 " --> pdb=" O LYS B 2 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N LEU B 4 " --> pdb=" O LYS A 409 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N PHE A 411 " --> pdb=" O LEU B 4 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N TYR B 6 " --> pdb=" O PHE A 411 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 311 through 314 removed outlier: 6.574A pdb=" N LEU A 402 " --> pdb=" O ILE A 179 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 208 through 210 Processing sheet with id=AA5, first strand: chain 'A' and resid 283 through 286 Processing sheet with id=AA6, first strand: chain 'A' and resid 304 through 305 Processing sheet with id=AA7, first strand: chain 'B' and resid 19 through 20 Processing sheet with id=AA8, first strand: chain 'B' and resid 91 through 95 removed outlier: 6.704A pdb=" N SER B 41 " --> pdb=" O VAL B 92 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N LYS B 94 " --> pdb=" O SER B 41 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL B 43 " --> pdb=" O LYS B 94 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N GLY B 42 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE B 142 " --> pdb=" O GLY B 42 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N VAL B 44 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N TRP B 139 " --> pdb=" O GLN B 222 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N LEU B 224 " --> pdb=" O TRP B 139 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N VAL B 141 " --> pdb=" O LEU B 224 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 425 through 426 272 hydrogen bonds defined for protein. 750 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 40 hydrogen bonds 80 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 30 stacking parallelities Total time for adding SS restraints: 2.69 Time building geometry restraints manager: 2.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1143 1.30 - 1.43: 2327 1.43 - 1.56: 4319 1.56 - 1.69: 80 1.69 - 1.81: 32 Bond restraints: 7901 Sorted by residual: bond pdb=" C PRO B 319 " pdb=" O PRO B 319 " ideal model delta sigma weight residual 1.234 1.178 0.056 1.14e-02 7.69e+03 2.38e+01 bond pdb=" C VAL B 278 " pdb=" O VAL B 278 " ideal model delta sigma weight residual 1.237 1.189 0.048 1.11e-02 8.12e+03 1.86e+01 bond pdb=" C GLU B 436 " pdb=" O GLU B 436 " ideal model delta sigma weight residual 1.242 1.202 0.039 1.00e-02 1.00e+04 1.56e+01 bond pdb=" C MET B 435 " pdb=" O MET B 435 " ideal model delta sigma weight residual 1.234 1.186 0.048 1.23e-02 6.61e+03 1.52e+01 bond pdb=" C TYR A 210 " pdb=" O TYR A 210 " ideal model delta sigma weight residual 1.235 1.194 0.042 1.13e-02 7.83e+03 1.37e+01 ... (remaining 7896 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 10475 1.74 - 3.47: 295 3.47 - 5.21: 57 5.21 - 6.94: 19 6.94 - 8.68: 7 Bond angle restraints: 10853 Sorted by residual: angle pdb=" CA TYR A 210 " pdb=" C TYR A 210 " pdb=" O TYR A 210 " ideal model delta sigma weight residual 120.33 113.09 7.24 1.08e+00 8.57e-01 4.49e+01 angle pdb=" C ILE A 208 " pdb=" N ARG A 209 " pdb=" CA ARG A 209 " ideal model delta sigma weight residual 121.24 112.72 8.52 1.44e+00 4.82e-01 3.50e+01 angle pdb=" C PRO B 438 " pdb=" CA PRO B 438 " pdb=" CB PRO B 438 " ideal model delta sigma weight residual 111.21 103.77 7.44 1.33e+00 5.65e-01 3.13e+01 angle pdb=" C ARG A 54 " pdb=" CA ARG A 54 " pdb=" CB ARG A 54 " ideal model delta sigma weight residual 110.90 102.22 8.68 1.58e+00 4.01e-01 3.02e+01 angle pdb=" CA LYS B 211 " pdb=" C LYS B 211 " pdb=" O LYS B 211 " ideal model delta sigma weight residual 120.55 114.74 5.81 1.06e+00 8.90e-01 3.00e+01 ... (remaining 10848 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 3839 17.68 - 35.35: 543 35.35 - 53.03: 205 53.03 - 70.70: 79 70.70 - 88.38: 23 Dihedral angle restraints: 4689 sinusoidal: 2274 harmonic: 2415 Sorted by residual: dihedral pdb=" O4' G C 20 " pdb=" C1' G C 20 " pdb=" N9 G C 20 " pdb=" C4 G C 20 " ideal model delta sinusoidal sigma weight residual -106.00 -169.38 63.38 1 1.70e+01 3.46e-03 1.83e+01 dihedral pdb=" C ARG A 209 " pdb=" N ARG A 209 " pdb=" CA ARG A 209 " pdb=" CB ARG A 209 " ideal model delta harmonic sigma weight residual -122.60 -112.69 -9.91 0 2.50e+00 1.60e-01 1.57e+01 dihedral pdb=" CA TRP A 219 " pdb=" C TRP A 219 " pdb=" N GLU A 220 " pdb=" CA GLU A 220 " ideal model delta harmonic sigma weight residual 180.00 -162.50 -17.50 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 4686 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1022 0.063 - 0.126: 142 0.126 - 0.189: 18 0.189 - 0.252: 6 0.252 - 0.314: 4 Chirality restraints: 1192 Sorted by residual: chirality pdb=" CA ILE B 274 " pdb=" N ILE B 274 " pdb=" C ILE B 274 " pdb=" CB ILE B 274 " both_signs ideal model delta sigma weight residual False 2.43 2.75 -0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" CA ARG A 209 " pdb=" N ARG A 209 " pdb=" C ARG A 209 " pdb=" CB ARG A 209 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" CA CYS A 58 " pdb=" N CYS A 58 " pdb=" C CYS A 58 " pdb=" CB CYS A 58 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.70e+00 ... (remaining 1189 not shown) Planarity restraints: 1218 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 437 " 0.017 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" C VAL B 437 " -0.059 2.00e-02 2.50e+03 pdb=" O VAL B 437 " 0.022 2.00e-02 2.50e+03 pdb=" N PRO B 438 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 49 " 0.015 2.00e-02 2.50e+03 3.19e-02 1.02e+01 pdb=" C ILE A 49 " -0.055 2.00e-02 2.50e+03 pdb=" O ILE A 49 " 0.021 2.00e-02 2.50e+03 pdb=" N GLU A 50 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 321 " -0.013 2.00e-02 2.50e+03 2.69e-02 7.21e+00 pdb=" C TYR B 321 " 0.046 2.00e-02 2.50e+03 pdb=" O TYR B 321 " -0.018 2.00e-02 2.50e+03 pdb=" N ASN B 322 " -0.016 2.00e-02 2.50e+03 ... (remaining 1215 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.38: 36 2.38 - 3.01: 4009 3.01 - 3.64: 12781 3.64 - 4.27: 20625 4.27 - 4.90: 32431 Nonbonded interactions: 69882 Sorted by model distance: nonbonded pdb=" O TYR B 321 " pdb=" OD1 ASN B 322 " model vdw 1.744 3.040 nonbonded pdb=" O ILE B 507 " pdb="MG MG B 601 " model vdw 1.831 2.170 nonbonded pdb=" OP2 A C 1 " pdb="MG MG B 601 " model vdw 1.963 2.170 nonbonded pdb=" ND2 ASN B 468 " pdb="MG MG B 601 " model vdw 2.020 2.250 nonbonded pdb=" NH1 ARG B 275 " pdb=" OD2 ASP B 458 " model vdw 2.075 3.120 ... (remaining 69877 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.250 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 24.660 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 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:12.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 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 : 0.004 0.056 7901 Z= 0.288 Angle : 0.729 8.679 10853 Z= 0.451 Chirality : 0.049 0.314 1192 Planarity : 0.006 0.076 1218 Dihedral : 20.290 88.377 3123 Min Nonbonded Distance : 1.744 Molprobity Statistics. All-atom Clashscore : 18.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.35 % Allowed : 24.32 % Favored : 71.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.28), residues: 803 helix: 0.58 (0.31), residues: 281 sheet: -0.37 (0.36), residues: 171 loop : -0.50 (0.31), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 320 HIS 0.003 0.001 HIS B 207 PHE 0.012 0.002 PHE A 343 TYR 0.028 0.002 TYR A 210 ARG 0.014 0.001 ARG A 250 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 105 time to evaluate : 1.053 Fit side-chains REVERT: A 50 GLU cc_start: 0.6667 (OUTLIER) cc_final: 0.6395 (tm-30) REVERT: B 270 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.7832 (ptpp) outliers start: 32 outliers final: 26 residues processed: 134 average time/residue: 1.4822 time to fit residues: 209.8092 Evaluate side-chains 126 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 98 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LYS Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 58 CYS Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 372 LYS Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 270 LYS Chi-restraints excluded: chain B residue 273 ASP Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 493 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 GLN B 296 ASN B 322 ASN B 371 ASN B 382 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.177761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.149475 restraints weight = 7078.988| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 1.29 r_work: 0.3709 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3608 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.0847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 7901 Z= 0.292 Angle : 0.601 5.790 10853 Z= 0.325 Chirality : 0.044 0.164 1192 Planarity : 0.005 0.048 1218 Dihedral : 17.296 79.799 1466 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 4.48 % Allowed : 21.88 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.28), residues: 803 helix: 0.51 (0.30), residues: 291 sheet: -0.61 (0.36), residues: 172 loop : -0.52 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 219 HIS 0.002 0.001 HIS B 16 PHE 0.017 0.002 PHE A 343 TYR 0.010 0.001 TYR A 330 ARG 0.004 0.001 ARG A 71 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 109 time to evaluate : 0.787 Fit side-chains REVERT: A 24 LYS cc_start: 0.6945 (OUTLIER) cc_final: 0.6626 (mptm) REVERT: A 280 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.7749 (mptp) REVERT: A 315 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8217 (mppt) REVERT: B 355 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.7826 (ttpp) outliers start: 33 outliers final: 14 residues processed: 133 average time/residue: 1.2236 time to fit residues: 172.1127 Evaluate side-chains 120 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 315 LYS Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 243 ARG Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 355 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 16 optimal weight: 0.1980 chunk 13 optimal weight: 9.9990 chunk 78 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 3 optimal weight: 0.2980 chunk 23 optimal weight: 0.9980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 GLN B 296 ASN B 371 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.180912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.154592 restraints weight = 7217.110| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 1.37 r_work: 0.3727 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3622 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.0914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7901 Z= 0.205 Angle : 0.544 5.382 10853 Z= 0.295 Chirality : 0.042 0.155 1192 Planarity : 0.004 0.041 1218 Dihedral : 17.024 77.259 1424 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.67 % Allowed : 22.96 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.28), residues: 803 helix: 0.69 (0.30), residues: 291 sheet: -0.62 (0.37), residues: 168 loop : -0.54 (0.30), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 219 HIS 0.002 0.001 HIS B 207 PHE 0.014 0.001 PHE B 78 TYR 0.012 0.001 TYR A 210 ARG 0.007 0.001 ARG A 71 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 113 time to evaluate : 0.797 Fit side-chains REVERT: A 24 LYS cc_start: 0.6864 (OUTLIER) cc_final: 0.6519 (mptm) REVERT: A 136 GLU cc_start: 0.7208 (mm-30) cc_final: 0.6897 (mm-30) REVERT: A 227 LEU cc_start: 0.8336 (mt) cc_final: 0.8104 (mt) REVERT: B 322 ASN cc_start: 0.6498 (OUTLIER) cc_final: 0.6101 (m-40) outliers start: 27 outliers final: 14 residues processed: 132 average time/residue: 1.3110 time to fit residues: 182.5026 Evaluate side-chains 122 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 243 ARG Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 322 ASN Chi-restraints excluded: chain B residue 339 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 46 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 63 optimal weight: 0.3980 chunk 3 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 74 optimal weight: 0.2980 chunk 10 optimal weight: 0.0070 chunk 19 optimal weight: 0.0000 overall best weight: 0.3002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN A 156 GLN ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 GLN B 296 ASN B 371 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.183087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.157098 restraints weight = 7270.586| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 1.37 r_work: 0.3764 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3660 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.1148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7901 Z= 0.172 Angle : 0.522 6.018 10853 Z= 0.282 Chirality : 0.041 0.145 1192 Planarity : 0.004 0.037 1218 Dihedral : 16.816 74.577 1419 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 4.35 % Allowed : 23.10 % Favored : 72.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.28), residues: 803 helix: 0.90 (0.31), residues: 289 sheet: -0.45 (0.38), residues: 161 loop : -0.61 (0.30), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 219 HIS 0.003 0.001 HIS B 207 PHE 0.012 0.001 PHE B 78 TYR 0.010 0.001 TYR A 210 ARG 0.009 0.001 ARG A 250 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 116 time to evaluate : 0.759 Fit side-chains REVERT: A 24 LYS cc_start: 0.7010 (OUTLIER) cc_final: 0.6619 (mptm) REVERT: A 136 GLU cc_start: 0.7152 (mm-30) cc_final: 0.6926 (mm-30) REVERT: A 227 LEU cc_start: 0.8287 (mt) cc_final: 0.8085 (mp) REVERT: A 352 LYS cc_start: 0.7491 (mmtm) cc_final: 0.7119 (mmmt) REVERT: B 322 ASN cc_start: 0.6396 (OUTLIER) cc_final: 0.6030 (m-40) REVERT: B 355 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.7892 (tttp) outliers start: 32 outliers final: 12 residues processed: 139 average time/residue: 1.1883 time to fit residues: 175.0016 Evaluate side-chains 121 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 106 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 322 ASN Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 355 LYS Chi-restraints excluded: chain B residue 435 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 82 optimal weight: 3.9990 chunk 76 optimal weight: 0.4980 chunk 73 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 chunk 19 optimal weight: 0.0060 chunk 67 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 340 HIS B 205 GLN B 296 ASN B 371 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.180940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.154802 restraints weight = 7192.482| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 1.40 r_work: 0.3732 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3626 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7901 Z= 0.209 Angle : 0.536 6.780 10853 Z= 0.288 Chirality : 0.042 0.156 1192 Planarity : 0.004 0.036 1218 Dihedral : 16.750 72.292 1416 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 4.08 % Allowed : 23.91 % Favored : 72.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.28), residues: 803 helix: 0.86 (0.30), residues: 290 sheet: -0.50 (0.38), residues: 161 loop : -0.55 (0.30), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 219 HIS 0.002 0.001 HIS A 340 PHE 0.014 0.001 PHE B 78 TYR 0.010 0.001 TYR A 330 ARG 0.007 0.001 ARG A 71 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 110 time to evaluate : 0.783 Fit side-chains REVERT: A 24 LYS cc_start: 0.7049 (OUTLIER) cc_final: 0.6700 (mptm) REVERT: A 227 LEU cc_start: 0.8335 (mt) cc_final: 0.8097 (mp) REVERT: A 352 LYS cc_start: 0.7517 (mmtm) cc_final: 0.7138 (mmmt) REVERT: A 363 LYS cc_start: 0.8080 (mtpp) cc_final: 0.7565 (mtmt) REVERT: B 355 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.7879 (tttp) outliers start: 30 outliers final: 16 residues processed: 132 average time/residue: 1.1332 time to fit residues: 159.0825 Evaluate side-chains 127 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 372 LYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 243 ARG Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 355 LYS Chi-restraints excluded: chain B residue 387 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 18 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 11 optimal weight: 0.2980 chunk 75 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 50 optimal weight: 0.3980 chunk 80 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 ASN B 296 ASN B 371 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.181449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.154938 restraints weight = 7143.416| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 1.37 r_work: 0.3735 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3632 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7901 Z= 0.207 Angle : 0.532 5.757 10853 Z= 0.287 Chirality : 0.042 0.151 1192 Planarity : 0.004 0.037 1218 Dihedral : 16.749 72.164 1416 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.94 % Allowed : 24.18 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.28), residues: 803 helix: 0.92 (0.31), residues: 290 sheet: -0.66 (0.37), residues: 168 loop : -0.46 (0.31), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 219 HIS 0.002 0.001 HIS B 207 PHE 0.014 0.001 PHE B 78 TYR 0.009 0.001 TYR A 330 ARG 0.007 0.001 ARG A 71 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 111 time to evaluate : 0.788 Fit side-chains REVERT: A 24 LYS cc_start: 0.6938 (OUTLIER) cc_final: 0.6576 (mptm) REVERT: A 51 LYS cc_start: 0.5812 (tptt) cc_final: 0.5497 (tppp) REVERT: A 227 LEU cc_start: 0.8334 (mt) cc_final: 0.8107 (mt) REVERT: A 287 MET cc_start: 0.8660 (OUTLIER) cc_final: 0.8295 (mmm) REVERT: A 352 LYS cc_start: 0.7484 (mmtm) cc_final: 0.7101 (mmmt) REVERT: B 355 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.7843 (tttp) outliers start: 29 outliers final: 14 residues processed: 132 average time/residue: 1.2028 time to fit residues: 168.0952 Evaluate side-chains 126 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 243 ARG Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 355 LYS Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 435 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 38 optimal weight: 0.0980 chunk 46 optimal weight: 0.8980 chunk 8 optimal weight: 0.0000 chunk 43 optimal weight: 0.9980 chunk 40 optimal weight: 0.4980 chunk 28 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 23 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 overall best weight: 0.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 GLN B 296 ASN B 371 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.182631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.156473 restraints weight = 7258.686| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 1.37 r_work: 0.3758 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3653 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7901 Z= 0.183 Angle : 0.525 7.119 10853 Z= 0.281 Chirality : 0.041 0.154 1192 Planarity : 0.004 0.036 1218 Dihedral : 16.704 72.240 1416 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.53 % Allowed : 24.86 % Favored : 71.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.28), residues: 803 helix: 0.94 (0.31), residues: 290 sheet: -0.48 (0.39), residues: 161 loop : -0.50 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 219 HIS 0.002 0.001 HIS B 207 PHE 0.013 0.001 PHE B 78 TYR 0.009 0.001 TYR A 210 ARG 0.010 0.000 ARG A 71 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 117 time to evaluate : 0.786 Fit side-chains REVERT: A 24 LYS cc_start: 0.7057 (OUTLIER) cc_final: 0.6693 (mptm) REVERT: A 51 LYS cc_start: 0.5708 (tptt) cc_final: 0.5390 (tppp) REVERT: A 227 LEU cc_start: 0.8330 (mt) cc_final: 0.8084 (mp) REVERT: A 287 MET cc_start: 0.8574 (OUTLIER) cc_final: 0.8274 (mmm) REVERT: A 363 LYS cc_start: 0.8069 (mtpp) cc_final: 0.7565 (mtmt) REVERT: B 322 ASN cc_start: 0.6328 (OUTLIER) cc_final: 0.5952 (m-40) REVERT: B 355 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.7848 (tttp) outliers start: 26 outliers final: 11 residues processed: 134 average time/residue: 1.2181 time to fit residues: 172.6815 Evaluate side-chains 125 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 322 ASN Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 355 LYS Chi-restraints excluded: chain B residue 387 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 38 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 78 optimal weight: 0.0670 chunk 12 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 ASN B 371 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.180608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.154110 restraints weight = 7230.818| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 1.34 r_work: 0.3725 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3622 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7901 Z= 0.231 Angle : 0.548 7.269 10853 Z= 0.293 Chirality : 0.042 0.154 1192 Planarity : 0.004 0.039 1218 Dihedral : 16.673 72.606 1415 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.26 % Allowed : 25.68 % Favored : 71.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.28), residues: 803 helix: 0.90 (0.31), residues: 290 sheet: -0.62 (0.38), residues: 168 loop : -0.40 (0.31), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 219 HIS 0.002 0.001 HIS B 207 PHE 0.015 0.002 PHE A 17 TYR 0.010 0.001 TYR A 233 ARG 0.009 0.001 ARG A 71 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 113 time to evaluate : 0.781 Fit side-chains REVERT: A 24 LYS cc_start: 0.6986 (OUTLIER) cc_final: 0.6639 (mptm) REVERT: A 51 LYS cc_start: 0.5739 (tptt) cc_final: 0.5412 (tppp) REVERT: A 92 MET cc_start: 0.6523 (ttt) cc_final: 0.6249 (ttm) REVERT: A 287 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.8351 (mmm) REVERT: A 363 LYS cc_start: 0.8077 (mtpp) cc_final: 0.7568 (mtmp) REVERT: B 211 LYS cc_start: 0.7466 (OUTLIER) cc_final: 0.6411 (mptm) REVERT: B 287 LYS cc_start: 0.7954 (mttp) cc_final: 0.7621 (mtmt) REVERT: B 322 ASN cc_start: 0.6327 (OUTLIER) cc_final: 0.5952 (m-40) REVERT: B 364 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.8091 (mtm180) outliers start: 24 outliers final: 10 residues processed: 130 average time/residue: 1.2754 time to fit residues: 175.5322 Evaluate side-chains 124 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 322 ASN Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 364 ARG Chi-restraints excluded: chain B residue 387 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 74 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 0.4980 chunk 61 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 73 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 ASN B 371 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.180143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.153664 restraints weight = 7281.901| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 1.34 r_work: 0.3719 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3614 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7901 Z= 0.238 Angle : 0.554 7.197 10853 Z= 0.297 Chirality : 0.042 0.156 1192 Planarity : 0.004 0.041 1218 Dihedral : 16.716 73.247 1415 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.12 % Allowed : 26.22 % Favored : 70.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.28), residues: 803 helix: 0.96 (0.31), residues: 284 sheet: -0.62 (0.37), residues: 168 loop : -0.38 (0.31), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 219 HIS 0.003 0.001 HIS A 160 PHE 0.016 0.002 PHE A 17 TYR 0.009 0.001 TYR A 330 ARG 0.009 0.001 ARG A 71 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 0.796 Fit side-chains REVERT: A 51 LYS cc_start: 0.5757 (tptt) cc_final: 0.5378 (tppp) REVERT: A 287 MET cc_start: 0.8667 (OUTLIER) cc_final: 0.8333 (mmm) REVERT: B 211 LYS cc_start: 0.7470 (OUTLIER) cc_final: 0.6447 (mptm) REVERT: B 322 ASN cc_start: 0.6255 (OUTLIER) cc_final: 0.5877 (m-40) REVERT: B 364 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.8072 (mtm180) outliers start: 23 outliers final: 11 residues processed: 127 average time/residue: 1.2701 time to fit residues: 170.5318 Evaluate side-chains 123 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 372 LYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 322 ASN Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 364 ARG Chi-restraints excluded: chain B residue 387 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 23 optimal weight: 0.0060 chunk 45 optimal weight: 5.9990 chunk 41 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 3 optimal weight: 0.5980 chunk 79 optimal weight: 0.5980 chunk 72 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 GLN B 296 ASN B 371 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.181770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.155296 restraints weight = 7279.432| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 1.38 r_work: 0.3748 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3647 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7901 Z= 0.200 Angle : 0.546 6.548 10853 Z= 0.292 Chirality : 0.041 0.152 1192 Planarity : 0.004 0.047 1218 Dihedral : 16.699 72.395 1415 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.45 % Allowed : 26.77 % Favored : 70.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.29), residues: 803 helix: 1.01 (0.31), residues: 284 sheet: -0.62 (0.38), residues: 168 loop : -0.41 (0.31), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 219 HIS 0.002 0.001 HIS B 207 PHE 0.016 0.001 PHE A 17 TYR 0.009 0.001 TYR A 233 ARG 0.013 0.001 ARG A 250 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.779 Fit side-chains REVERT: A 51 LYS cc_start: 0.5818 (tptt) cc_final: 0.5459 (tppp) REVERT: A 92 MET cc_start: 0.6546 (ttt) cc_final: 0.6336 (ttm) REVERT: A 287 MET cc_start: 0.8616 (OUTLIER) cc_final: 0.8310 (mmm) REVERT: A 363 LYS cc_start: 0.8065 (mtpp) cc_final: 0.7550 (mtmp) REVERT: A 406 LYS cc_start: 0.7832 (mmmt) cc_final: 0.7510 (mmtt) REVERT: B 211 LYS cc_start: 0.7474 (OUTLIER) cc_final: 0.6469 (mptm) REVERT: B 287 LYS cc_start: 0.7966 (mttp) cc_final: 0.7656 (mtmt) REVERT: B 322 ASN cc_start: 0.6207 (OUTLIER) cc_final: 0.5852 (m-40) outliers start: 18 outliers final: 11 residues processed: 125 average time/residue: 1.2436 time to fit residues: 164.5328 Evaluate side-chains 125 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 372 LYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 322 ASN Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 387 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 12 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 chunk 72 optimal weight: 0.5980 chunk 84 optimal weight: 0.5980 chunk 74 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 GLN B 296 ASN B 371 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.180323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.153536 restraints weight = 7198.853| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 1.37 r_work: 0.3722 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3617 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7901 Z= 0.242 Angle : 0.564 6.248 10853 Z= 0.301 Chirality : 0.042 0.156 1192 Planarity : 0.004 0.054 1218 Dihedral : 16.674 73.839 1415 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.31 % Allowed : 27.04 % Favored : 70.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.28), residues: 803 helix: 0.96 (0.31), residues: 284 sheet: -0.59 (0.37), residues: 168 loop : -0.44 (0.31), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 219 HIS 0.003 0.001 HIS A 160 PHE 0.017 0.002 PHE A 17 TYR 0.009 0.001 TYR A 330 ARG 0.013 0.001 ARG A 250 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6656.11 seconds wall clock time: 113 minutes 57.40 seconds (6837.40 seconds total)