Starting phenix.real_space_refine on Tue Mar 11 18:45:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7p1j_13162/03_2025/7p1j_13162.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p1j_13162/03_2025/7p1j_13162.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7p1j_13162/03_2025/7p1j_13162.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p1j_13162/03_2025/7p1j_13162.map" model { file = "/net/cci-nas-00/data/ceres_data/7p1j_13162/03_2025/7p1j_13162.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p1j_13162/03_2025/7p1j_13162.cif" } resolution = 3.04 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 38 5.16 5 C 4334 2.51 5 N 1034 2.21 5 O 1096 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6502 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 3251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3251 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 20, 'TRANS': 413} Chain breaks: 1 Chain: "A" Number of atoms: 3251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3251 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 20, 'TRANS': 413} Chain breaks: 1 Time building chain proxies: 6.15, per 1000 atoms: 0.95 Number of scatterers: 6502 At special positions: 0 Unit cell: (119.312, 90.2625, 85.075, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 38 16.00 O 1096 8.00 N 1034 7.00 C 4334 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: 1.75 Conformation dependent library (CDL) restraints added in 1.2 seconds 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1544 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 0 sheets defined 83.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'B' and resid 80 through 104 removed outlier: 4.203A pdb=" N VAL B 86 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ILE B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 134 removed outlier: 4.216A pdb=" N GLY B 132 " --> pdb=" O GLY B 128 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE B 134 " --> pdb=" O LEU B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 157 removed outlier: 4.490A pdb=" N GLY B 147 " --> pdb=" O PRO B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 162 Processing helix chain 'B' and resid 168 through 190 Processing helix chain 'B' and resid 194 through 199 Processing helix chain 'B' and resid 200 through 223 Proline residue: B 210 - end of helix Processing helix chain 'B' and resid 229 through 241 Processing helix chain 'B' and resid 244 through 259 removed outlier: 4.147A pdb=" N VAL B 248 " --> pdb=" O SER B 244 " (cutoff:3.500A) Proline residue: B 250 - end of helix Processing helix chain 'B' and resid 265 through 274 Processing helix chain 'B' and resid 276 through 293 removed outlier: 4.057A pdb=" N LEU B 280 " --> pdb=" O PHE B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 321 removed outlier: 3.664A pdb=" N PHE B 321 " --> pdb=" O LEU B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 357 Processing helix chain 'B' and resid 360 through 377 removed outlier: 3.966A pdb=" N LEU B 364 " --> pdb=" O GLY B 360 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU B 367 " --> pdb=" O GLY B 363 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TRP B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 404 removed outlier: 3.561A pdb=" N LYS B 386 " --> pdb=" O THR B 382 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N VAL B 387 " --> pdb=" O ASP B 383 " (cutoff:3.500A) Proline residue: B 397 - end of helix Processing helix chain 'B' and resid 417 through 439 Processing helix chain 'B' and resid 446 through 455 removed outlier: 3.888A pdb=" N ILE B 450 " --> pdb=" O ILE B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 478 removed outlier: 4.214A pdb=" N ALA B 464 " --> pdb=" O ALA B 460 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER B 476 " --> pdb=" O ASP B 472 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N HIS B 477 " --> pdb=" O THR B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 516 removed outlier: 3.529A pdb=" N ALA B 501 " --> pdb=" O ILE B 497 " (cutoff:3.500A) Proline residue: B 502 - end of helix Proline residue: B 513 - end of helix removed outlier: 3.714A pdb=" N LEU B 516 " --> pdb=" O GLY B 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 105 removed outlier: 4.099A pdb=" N VAL A 86 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ILE A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL A 103 " --> pdb=" O VAL A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 134 removed outlier: 4.207A pdb=" N GLY A 132 " --> pdb=" O GLY A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 157 removed outlier: 4.392A pdb=" N GLY A 147 " --> pdb=" O PRO A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 165 removed outlier: 3.961A pdb=" N ASN A 164 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE A 165 " --> pdb=" O ILE A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 191 Processing helix chain 'A' and resid 194 through 199 Processing helix chain 'A' and resid 200 through 223 Proline residue: A 210 - end of helix Processing helix chain 'A' and resid 229 through 241 Processing helix chain 'A' and resid 244 through 259 removed outlier: 3.688A pdb=" N VAL A 248 " --> pdb=" O SER A 244 " (cutoff:3.500A) Proline residue: A 250 - end of helix removed outlier: 3.550A pdb=" N GLY A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 293 removed outlier: 4.238A pdb=" N SER A 275 " --> pdb=" O MET A 271 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N PHE A 276 " --> pdb=" O ALA A 272 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ASP A 277 " --> pdb=" O ALA A 273 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ASP A 278 " --> pdb=" O GLY A 274 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ILE A 279 " --> pdb=" O SER A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 322 removed outlier: 3.806A pdb=" N PHE A 322 " --> pdb=" O VAL A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 357 removed outlier: 3.501A pdb=" N PHE A 340 " --> pdb=" O TRP A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 377 removed outlier: 4.015A pdb=" N LEU A 364 " --> pdb=" O GLY A 360 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU A 367 " --> pdb=" O GLY A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 405 removed outlier: 4.250A pdb=" N VAL A 384 " --> pdb=" O THR A 380 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS A 386 " --> pdb=" O THR A 382 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N VAL A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) Proline residue: A 397 - end of helix Processing helix chain 'A' and resid 417 through 439 removed outlier: 3.527A pdb=" N VAL A 439 " --> pdb=" O THR A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 455 removed outlier: 3.942A pdb=" N ILE A 450 " --> pdb=" O ILE A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 478 removed outlier: 4.000A pdb=" N ALA A 464 " --> pdb=" O ALA A 460 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER A 476 " --> pdb=" O ASP A 472 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N HIS A 477 " --> pdb=" O THR A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 516 removed outlier: 3.614A pdb=" N ALA A 501 " --> pdb=" O ILE A 497 " (cutoff:3.500A) Proline residue: A 502 - end of helix Proline residue: A 513 - end of helix removed outlier: 3.704A pdb=" N LEU A 516 " --> pdb=" O GLY A 512 " (cutoff:3.500A) 498 hydrogen bonds defined for protein. 1488 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.29 Time building geometry restraints manager: 2.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1966 1.34 - 1.46: 1378 1.46 - 1.58: 3244 1.58 - 1.69: 0 1.69 - 1.81: 58 Bond restraints: 6646 Sorted by residual: bond pdb=" N VAL B 158 " pdb=" CA VAL B 158 " ideal model delta sigma weight residual 1.454 1.461 -0.007 7.70e-03 1.69e+04 8.11e-01 bond pdb=" C TYR A 325 " pdb=" N PHE A 326 " ideal model delta sigma weight residual 1.332 1.344 -0.011 1.50e-02 4.44e+03 5.57e-01 bond pdb=" CA LEU A 208 " pdb=" C LEU A 208 " ideal model delta sigma weight residual 1.519 1.527 -0.008 1.22e-02 6.72e+03 4.58e-01 bond pdb=" C PHE A 326 " pdb=" N PRO A 327 " ideal model delta sigma weight residual 1.334 1.349 -0.015 2.34e-02 1.83e+03 4.04e-01 bond pdb=" N VAL A 158 " pdb=" CA VAL A 158 " ideal model delta sigma weight residual 1.461 1.454 0.007 1.23e-02 6.61e+03 3.42e-01 ... (remaining 6641 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 8933 1.73 - 3.47: 97 3.47 - 5.20: 17 5.20 - 6.93: 3 6.93 - 8.66: 2 Bond angle restraints: 9052 Sorted by residual: angle pdb=" C VAL A 248 " pdb=" N VAL A 249 " pdb=" CA VAL A 249 " ideal model delta sigma weight residual 120.33 122.82 -2.49 8.00e-01 1.56e+00 9.68e+00 angle pdb=" CA LEU B 412 " pdb=" CB LEU B 412 " pdb=" CG LEU B 412 " ideal model delta sigma weight residual 116.30 124.96 -8.66 3.50e+00 8.16e-02 6.13e+00 angle pdb=" CA LEU A 412 " pdb=" CB LEU A 412 " pdb=" CG LEU A 412 " ideal model delta sigma weight residual 116.30 124.94 -8.64 3.50e+00 8.16e-02 6.09e+00 angle pdb=" C ALA A 460 " pdb=" N THR A 461 " pdb=" CA THR A 461 " ideal model delta sigma weight residual 121.54 126.18 -4.64 1.91e+00 2.74e-01 5.91e+00 angle pdb=" C VAL A 249 " pdb=" CA VAL A 249 " pdb=" CB VAL A 249 " ideal model delta sigma weight residual 114.00 111.22 2.78 1.31e+00 5.83e-01 4.51e+00 ... (remaining 9047 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.46: 3577 11.46 - 22.92: 186 22.92 - 34.38: 62 34.38 - 45.84: 28 45.84 - 57.30: 5 Dihedral angle restraints: 3858 sinusoidal: 1436 harmonic: 2422 Sorted by residual: dihedral pdb=" N ARG A 176 " pdb=" CA ARG A 176 " pdb=" CB ARG A 176 " pdb=" CG ARG A 176 " ideal model delta sinusoidal sigma weight residual -60.00 -117.30 57.30 3 1.50e+01 4.44e-03 9.43e+00 dihedral pdb=" N PHE A 356 " pdb=" CA PHE A 356 " pdb=" CB PHE A 356 " pdb=" CG PHE A 356 " ideal model delta sinusoidal sigma weight residual -180.00 -127.72 -52.28 3 1.50e+01 4.44e-03 9.10e+00 dihedral pdb=" N TRP A 171 " pdb=" CA TRP A 171 " pdb=" CB TRP A 171 " pdb=" CG TRP A 171 " ideal model delta sinusoidal sigma weight residual -60.00 -108.02 48.02 3 1.50e+01 4.44e-03 8.58e+00 ... (remaining 3855 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 661 0.023 - 0.045: 245 0.045 - 0.068: 152 0.068 - 0.090: 35 0.090 - 0.113: 25 Chirality restraints: 1118 Sorted by residual: chirality pdb=" CA ILE B 167 " pdb=" N ILE B 167 " pdb=" C ILE B 167 " pdb=" CB ILE B 167 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.18e-01 chirality pdb=" CG LEU A 412 " pdb=" CB LEU A 412 " pdb=" CD1 LEU A 412 " pdb=" CD2 LEU A 412 " both_signs ideal model delta sigma weight residual False -2.59 -2.48 -0.11 2.00e-01 2.50e+01 3.11e-01 chirality pdb=" CA PRO B 210 " pdb=" N PRO B 210 " pdb=" C PRO B 210 " pdb=" CB PRO B 210 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.01e-01 ... (remaining 1115 not shown) Planarity restraints: 1094 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 512 " 0.028 5.00e-02 4.00e+02 4.17e-02 2.79e+00 pdb=" N PRO A 513 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 513 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 513 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 109 " -0.021 5.00e-02 4.00e+02 3.19e-02 1.63e+00 pdb=" N PRO A 110 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 110 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 110 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 512 " -0.021 5.00e-02 4.00e+02 3.13e-02 1.57e+00 pdb=" N PRO B 513 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO B 513 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 513 " -0.017 5.00e-02 4.00e+02 ... (remaining 1091 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.82: 1902 2.82 - 3.34: 6870 3.34 - 3.86: 10382 3.86 - 4.38: 10917 4.38 - 4.90: 19952 Nonbonded interactions: 50023 Sorted by model distance: nonbonded pdb=" O PHE A 153 " pdb=" ND2 ASN A 157 " model vdw 2.305 3.120 nonbonded pdb=" O PHE A 444 " pdb=" NZ LYS A 449 " model vdw 2.314 3.120 nonbonded pdb=" O PHE B 444 " pdb=" NZ LYS B 449 " model vdw 2.315 3.120 nonbonded pdb=" OG SER B 106 " pdb=" OE1 GLU B 107 " model vdw 2.322 3.040 nonbonded pdb=" O PHE B 153 " pdb=" ND2 ASN B 157 " model vdw 2.372 3.120 ... (remaining 50018 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 2.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 25.110 Find NCS groups from input model: 0.320 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:3.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 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 : 0.002 0.018 6646 Z= 0.104 Angle : 0.476 8.663 9052 Z= 0.238 Chirality : 0.034 0.113 1118 Planarity : 0.003 0.042 1094 Dihedral : 8.895 57.299 2314 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.29 % Allowed : 7.45 % Favored : 90.26 % 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: 2.14 (0.30), residues: 860 helix: 2.30 (0.20), residues: 672 sheet: None (None), residues: 0 loop : -2.03 (0.49), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 392 HIS 0.001 0.000 HIS A 477 PHE 0.004 0.001 PHE B 358 TYR 0.004 0.001 TYR B 436 ARG 0.001 0.000 ARG B 413 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 231 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 97 TRP cc_start: 0.7497 (t60) cc_final: 0.7247 (t-100) REVERT: B 165 ILE cc_start: 0.8534 (OUTLIER) cc_final: 0.8235 (mp) REVERT: B 214 GLU cc_start: 0.8011 (tt0) cc_final: 0.7423 (tp30) REVERT: B 440 CYS cc_start: 0.7345 (p) cc_final: 0.6981 (m) REVERT: B 454 PHE cc_start: 0.8504 (m-10) cc_final: 0.8273 (m-80) REVERT: A 433 LEU cc_start: 0.8977 (mm) cc_final: 0.8735 (mm) outliers start: 16 outliers final: 2 residues processed: 242 average time/residue: 0.1523 time to fit residues: 50.9785 Evaluate side-chains 133 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 130 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain A residue 226 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 43 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 chunk 67 optimal weight: 20.0000 chunk 26 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.097278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.081209 restraints weight = 30318.822| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 4.79 r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6646 Z= 0.267 Angle : 0.806 11.361 9052 Z= 0.387 Chirality : 0.045 0.350 1118 Planarity : 0.005 0.079 1094 Dihedral : 4.112 31.858 910 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 5.16 % Allowed : 18.48 % Favored : 76.36 % 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: 1.96 (0.30), residues: 860 helix: 2.19 (0.20), residues: 668 sheet: None (None), residues: 0 loop : -2.11 (0.48), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 377 HIS 0.002 0.001 HIS A 169 PHE 0.013 0.002 PHE B 451 TYR 0.009 0.001 TYR B 355 ARG 0.011 0.001 ARG A 431 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 142 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 277 ASP cc_start: 0.8815 (t70) cc_final: 0.8494 (t0) REVERT: B 424 LEU cc_start: 0.9135 (mt) cc_final: 0.8913 (mp) REVERT: B 454 PHE cc_start: 0.8564 (m-10) cc_final: 0.8197 (m-80) REVERT: B 466 ILE cc_start: 0.9390 (mt) cc_final: 0.9131 (tt) REVERT: A 122 TYR cc_start: 0.7123 (OUTLIER) cc_final: 0.6671 (t80) REVERT: A 326 PHE cc_start: 0.7456 (m-80) cc_final: 0.7213 (m-80) REVERT: A 332 ASP cc_start: 0.8351 (t0) cc_final: 0.8127 (t0) REVERT: A 433 LEU cc_start: 0.9155 (mm) cc_final: 0.8931 (mm) REVERT: A 454 PHE cc_start: 0.8650 (m-10) cc_final: 0.8410 (m-80) REVERT: A 490 LEU cc_start: 0.8747 (mt) cc_final: 0.8443 (mt) outliers start: 36 outliers final: 24 residues processed: 167 average time/residue: 0.1403 time to fit residues: 34.0539 Evaluate side-chains 143 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 118 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 122 TYR Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 356 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 29 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 chunk 45 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 54 optimal weight: 0.0470 overall best weight: 1.0082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.098525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.083660 restraints weight = 31419.381| |-----------------------------------------------------------------------------| r_work (start): 0.3918 rms_B_bonded: 4.48 r_work (final): 0.3918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.4079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6646 Z= 0.193 Angle : 0.792 15.894 9052 Z= 0.358 Chirality : 0.043 0.260 1118 Planarity : 0.004 0.041 1094 Dihedral : 4.268 29.659 910 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 5.16 % Allowed : 18.91 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.51 (0.30), residues: 860 helix: 1.88 (0.20), residues: 670 sheet: None (None), residues: 0 loop : -2.33 (0.46), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 377 HIS 0.001 0.001 HIS A 169 PHE 0.020 0.001 PHE A 322 TYR 0.010 0.001 TYR B 485 ARG 0.003 0.000 ARG B 431 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 129 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 288 CYS cc_start: 0.8293 (t) cc_final: 0.8039 (t) REVERT: B 454 PHE cc_start: 0.8465 (m-10) cc_final: 0.8092 (m-80) REVERT: B 466 ILE cc_start: 0.9311 (mt) cc_final: 0.9048 (tt) REVERT: A 122 TYR cc_start: 0.6773 (OUTLIER) cc_final: 0.6428 (t80) REVERT: A 433 LEU cc_start: 0.9087 (mm) cc_final: 0.8805 (mm) outliers start: 36 outliers final: 22 residues processed: 152 average time/residue: 0.1336 time to fit residues: 29.8679 Evaluate side-chains 138 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 122 TYR Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 289 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 39 optimal weight: 0.0050 chunk 79 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 59 optimal weight: 0.0170 chunk 31 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 54 optimal weight: 7.9990 chunk 27 optimal weight: 8.9990 chunk 40 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 overall best weight: 0.8038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 157 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.098974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.083077 restraints weight = 31991.064| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 4.95 r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.4366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6646 Z= 0.190 Angle : 0.741 13.518 9052 Z= 0.342 Chirality : 0.041 0.273 1118 Planarity : 0.004 0.041 1094 Dihedral : 4.295 29.819 910 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 5.87 % Allowed : 18.62 % Favored : 75.50 % 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: 1.36 (0.30), residues: 860 helix: 1.77 (0.20), residues: 670 sheet: None (None), residues: 0 loop : -2.36 (0.46), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 377 HIS 0.001 0.000 HIS A 169 PHE 0.011 0.001 PHE A 285 TYR 0.013 0.001 TYR B 485 ARG 0.002 0.000 ARG B 431 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 128 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 214 GLU cc_start: 0.8524 (tt0) cc_final: 0.7786 (mm-30) REVERT: B 454 PHE cc_start: 0.8451 (m-10) cc_final: 0.8051 (m-80) REVERT: A 122 TYR cc_start: 0.6948 (OUTLIER) cc_final: 0.6560 (t80) REVERT: A 433 LEU cc_start: 0.9160 (mm) cc_final: 0.8852 (mm) outliers start: 41 outliers final: 25 residues processed: 153 average time/residue: 0.1864 time to fit residues: 40.8748 Evaluate side-chains 134 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 108 time to evaluate : 2.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 122 TYR Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 406 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 73 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 42 optimal weight: 9.9990 chunk 26 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 18 optimal weight: 0.0770 chunk 65 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 overall best weight: 0.8940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.098501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.083952 restraints weight = 31266.621| |-----------------------------------------------------------------------------| r_work (start): 0.3927 rms_B_bonded: 4.46 r_work (final): 0.3927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.4566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6646 Z= 0.185 Angle : 0.759 11.399 9052 Z= 0.352 Chirality : 0.042 0.270 1118 Planarity : 0.004 0.041 1094 Dihedral : 4.307 29.832 910 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 6.16 % Allowed : 19.91 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.24 (0.30), residues: 860 helix: 1.64 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -2.41 (0.48), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 377 HIS 0.001 0.001 HIS B 477 PHE 0.009 0.001 PHE A 451 TYR 0.044 0.002 TYR B 485 ARG 0.003 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 114 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 165 ILE cc_start: 0.8442 (OUTLIER) cc_final: 0.8231 (mp) REVERT: B 214 GLU cc_start: 0.8496 (tt0) cc_final: 0.7798 (mm-30) REVERT: B 377 TRP cc_start: 0.6618 (t-100) cc_final: 0.6327 (t-100) REVERT: B 454 PHE cc_start: 0.8424 (m-10) cc_final: 0.8026 (m-80) REVERT: B 485 TYR cc_start: 0.8499 (m-80) cc_final: 0.8175 (m-80) REVERT: A 122 TYR cc_start: 0.6746 (OUTLIER) cc_final: 0.6414 (t80) REVERT: A 235 MET cc_start: 0.6706 (mtt) cc_final: 0.6250 (mtt) REVERT: A 332 ASP cc_start: 0.7819 (t0) cc_final: 0.7578 (t0) REVERT: A 433 LEU cc_start: 0.9106 (mm) cc_final: 0.8782 (mm) REVERT: A 490 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8789 (mt) outliers start: 43 outliers final: 27 residues processed: 142 average time/residue: 0.1421 time to fit residues: 28.9776 Evaluate side-chains 140 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 110 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 122 TYR Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 490 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 25 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 22 optimal weight: 8.9990 chunk 4 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 2 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.097165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.082993 restraints weight = 30985.659| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 4.27 r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.4744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6646 Z= 0.192 Angle : 0.750 12.613 9052 Z= 0.352 Chirality : 0.041 0.185 1118 Planarity : 0.004 0.042 1094 Dihedral : 4.318 30.015 910 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 6.02 % Allowed : 20.49 % Favored : 73.50 % 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: 1.26 (0.30), residues: 860 helix: 1.65 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -2.44 (0.48), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 232 HIS 0.002 0.000 HIS A 169 PHE 0.014 0.001 PHE B 451 TYR 0.043 0.002 TYR B 485 ARG 0.004 0.000 ARG A 375 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 113 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 MET cc_start: 0.8215 (mtp) cc_final: 0.7993 (mtm) REVERT: B 214 GLU cc_start: 0.8555 (tt0) cc_final: 0.7823 (mm-30) REVERT: B 377 TRP cc_start: 0.6653 (t-100) cc_final: 0.6337 (t-100) REVERT: B 454 PHE cc_start: 0.8452 (m-10) cc_final: 0.8047 (m-80) REVERT: A 122 TYR cc_start: 0.6885 (OUTLIER) cc_final: 0.6503 (t80) REVERT: A 181 SER cc_start: 0.7553 (OUTLIER) cc_final: 0.7321 (t) REVERT: A 433 LEU cc_start: 0.9127 (mm) cc_final: 0.8819 (mm) REVERT: A 490 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8752 (mt) outliers start: 42 outliers final: 28 residues processed: 141 average time/residue: 0.1443 time to fit residues: 29.4929 Evaluate side-chains 137 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 106 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 122 TYR Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 490 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 36 optimal weight: 8.9990 chunk 69 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 42 optimal weight: 20.0000 chunk 26 optimal weight: 0.8980 chunk 5 optimal weight: 8.9990 chunk 56 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.098134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.083455 restraints weight = 30987.079| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 4.48 r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.4872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6646 Z= 0.177 Angle : 0.765 12.519 9052 Z= 0.354 Chirality : 0.043 0.295 1118 Planarity : 0.004 0.041 1094 Dihedral : 4.317 30.049 910 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 5.30 % Allowed : 21.78 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.22 (0.30), residues: 860 helix: 1.62 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -2.42 (0.48), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 392 HIS 0.001 0.000 HIS A 169 PHE 0.021 0.001 PHE A 322 TYR 0.046 0.002 TYR B 485 ARG 0.004 0.000 ARG A 375 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 111 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 MET cc_start: 0.8018 (mtp) cc_final: 0.7776 (mtm) REVERT: B 214 GLU cc_start: 0.8559 (tt0) cc_final: 0.7786 (tp30) REVERT: B 377 TRP cc_start: 0.6618 (t-100) cc_final: 0.6254 (t-100) REVERT: B 454 PHE cc_start: 0.8437 (m-10) cc_final: 0.8038 (m-80) REVERT: A 122 TYR cc_start: 0.6802 (OUTLIER) cc_final: 0.6463 (t80) REVERT: A 433 LEU cc_start: 0.9109 (mm) cc_final: 0.8783 (mm) outliers start: 37 outliers final: 26 residues processed: 135 average time/residue: 0.1365 time to fit residues: 26.7411 Evaluate side-chains 136 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 109 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 122 TYR Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 461 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 13 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 35 optimal weight: 7.9990 chunk 8 optimal weight: 0.3980 chunk 43 optimal weight: 8.9990 chunk 7 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 39 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.098092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.083576 restraints weight = 31551.520| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 4.40 r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.4965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6646 Z= 0.173 Angle : 0.762 13.267 9052 Z= 0.353 Chirality : 0.040 0.198 1118 Planarity : 0.004 0.041 1094 Dihedral : 4.275 29.938 910 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 5.16 % Allowed : 22.21 % Favored : 72.64 % 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: 1.26 (0.30), residues: 860 helix: 1.66 (0.20), residues: 678 sheet: None (None), residues: 0 loop : -2.43 (0.47), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 392 HIS 0.001 0.000 HIS A 169 PHE 0.020 0.001 PHE A 322 TYR 0.042 0.002 TYR B 485 ARG 0.003 0.000 ARG A 375 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 114 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 145 LEU cc_start: 0.8627 (mp) cc_final: 0.8419 (mp) REVERT: B 214 GLU cc_start: 0.8548 (tt0) cc_final: 0.7780 (tp30) REVERT: B 377 TRP cc_start: 0.6651 (t-100) cc_final: 0.6317 (t-100) REVERT: B 454 PHE cc_start: 0.8436 (m-10) cc_final: 0.8003 (m-80) REVERT: A 122 TYR cc_start: 0.6785 (OUTLIER) cc_final: 0.6444 (t80) REVERT: A 291 MET cc_start: 0.7058 (ppp) cc_final: 0.6855 (ppp) REVERT: A 433 LEU cc_start: 0.9100 (mm) cc_final: 0.8787 (mm) outliers start: 36 outliers final: 26 residues processed: 137 average time/residue: 0.1323 time to fit residues: 26.3783 Evaluate side-chains 139 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 112 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 122 TYR Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 461 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 28 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 32 optimal weight: 9.9990 chunk 8 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 17 optimal weight: 0.0970 chunk 83 optimal weight: 5.9990 chunk 56 optimal weight: 0.6980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 157 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.097930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.083819 restraints weight = 31120.233| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 4.29 r_work (final): 0.3911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.5054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6646 Z= 0.176 Angle : 0.790 13.457 9052 Z= 0.367 Chirality : 0.042 0.221 1118 Planarity : 0.004 0.041 1094 Dihedral : 4.303 29.875 910 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 4.30 % Allowed : 23.64 % Favored : 72.06 % 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: 1.20 (0.30), residues: 860 helix: 1.61 (0.20), residues: 678 sheet: None (None), residues: 0 loop : -2.36 (0.48), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 232 HIS 0.001 0.000 HIS A 169 PHE 0.020 0.001 PHE A 322 TYR 0.043 0.001 TYR B 485 ARG 0.004 0.000 ARG B 413 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 118 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 214 GLU cc_start: 0.8559 (tt0) cc_final: 0.7622 (tp30) REVERT: B 377 TRP cc_start: 0.6635 (t-100) cc_final: 0.6302 (t-100) REVERT: B 454 PHE cc_start: 0.8426 (m-10) cc_final: 0.8025 (m-80) REVERT: A 122 TYR cc_start: 0.6879 (OUTLIER) cc_final: 0.6525 (t80) REVERT: A 433 LEU cc_start: 0.9066 (mm) cc_final: 0.8730 (mm) REVERT: A 487 MET cc_start: 0.8286 (tmm) cc_final: 0.8045 (tmm) outliers start: 30 outliers final: 27 residues processed: 138 average time/residue: 0.1312 time to fit residues: 26.4707 Evaluate side-chains 139 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 111 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 122 TYR Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 461 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 9 optimal weight: 0.8980 chunk 34 optimal weight: 6.9990 chunk 35 optimal weight: 8.9990 chunk 28 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 chunk 81 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.096113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.081251 restraints weight = 31978.608| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 4.32 r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.5238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 6646 Z= 0.270 Angle : 0.819 12.773 9052 Z= 0.390 Chirality : 0.043 0.202 1118 Planarity : 0.004 0.043 1094 Dihedral : 4.482 30.659 910 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 4.01 % Allowed : 24.64 % Favored : 71.35 % 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: 1.17 (0.30), residues: 860 helix: 1.54 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -2.24 (0.50), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 392 HIS 0.003 0.001 HIS A 477 PHE 0.015 0.002 PHE A 322 TYR 0.041 0.002 TYR B 485 ARG 0.007 0.001 ARG A 156 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 110 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 214 GLU cc_start: 0.8619 (tt0) cc_final: 0.7841 (tp30) REVERT: B 377 TRP cc_start: 0.6900 (t-100) cc_final: 0.6461 (t-100) REVERT: B 454 PHE cc_start: 0.8495 (m-10) cc_final: 0.8123 (m-80) REVERT: A 122 TYR cc_start: 0.6801 (OUTLIER) cc_final: 0.6475 (t80) REVERT: A 433 LEU cc_start: 0.9091 (mm) cc_final: 0.8750 (mm) outliers start: 28 outliers final: 26 residues processed: 125 average time/residue: 0.1381 time to fit residues: 25.1293 Evaluate side-chains 135 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 108 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 122 TYR Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 406 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 85 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 78 optimal weight: 8.9990 chunk 55 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 5 optimal weight: 0.4980 chunk 1 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.098052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.083432 restraints weight = 32240.500| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 4.29 r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.5256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6646 Z= 0.186 Angle : 0.799 13.381 9052 Z= 0.370 Chirality : 0.042 0.196 1118 Planarity : 0.004 0.042 1094 Dihedral : 4.411 29.885 910 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 4.58 % Allowed : 23.93 % Favored : 71.49 % 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: 1.21 (0.30), residues: 860 helix: 1.59 (0.20), residues: 678 sheet: None (None), residues: 0 loop : -2.28 (0.49), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 392 HIS 0.001 0.000 HIS A 169 PHE 0.017 0.001 PHE A 322 TYR 0.043 0.002 TYR B 485 ARG 0.005 0.001 ARG A 431 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3508.50 seconds wall clock time: 60 minutes 49.29 seconds (3649.29 seconds total)