Starting phenix.real_space_refine on Tue Feb 11 19:16:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7p1j_13162/02_2025/7p1j_13162.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p1j_13162/02_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_13162/02_2025/7p1j_13162.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p1j_13162/02_2025/7p1j_13162.map" model { file = "/net/cci-nas-00/data/ceres_data/7p1j_13162/02_2025/7p1j_13162.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p1j_13162/02_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 4.69, per 1000 atoms: 0.72 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: 1.54 Conformation dependent library (CDL) restraints added in 963.5 milliseconds 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: 0.57 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: 1.85 Time building geometry restraints manager: 1.80 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: 0.03 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: 0.910 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.180 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.450 ------------------------------------------------------------------------------- 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 : 0.747 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: 0.1532 time to fit residues: 50.7106 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 : 0.710 ------------------------------------------------------------------------------- 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 = 0.081208 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 : 0.674 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: 0.9136 (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: 0.9389 (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: 0.8128 (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: 0.8411 (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: 0.1319 time to fit residues: 31.6212 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 : 0.703 ------------------------------------------------------------------------------- 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: 7.9990 chunk 45 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 54 optimal weight: 8.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.4187 r_free = 0.4187 target = 0.097248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.081301 restraints weight = 31067.129| |-----------------------------------------------------------------------------| r_work (start): 0.3884 rms_B_bonded: 4.99 r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.4088 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= 0.210 Angle : 0.793 15.219 9052 Z= 0.361 Chirality : 0.044 0.249 1118 Planarity : 0.004 0.041 1094 Dihedral : 4.285 29.888 910 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 5.59 % Allowed : 18.77 % Favored : 75.64 % 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: 1.54 (0.30), residues: 860 helix: 1.88 (0.20), residues: 672 sheet: None (None), residues: 0 loop : -2.30 (0.47), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 377 HIS 0.002 0.001 HIS A 169 PHE 0.018 0.001 PHE A 322 TYR 0.010 0.001 TYR B 485 ARG 0.003 0.000 ARG A 156 *********************** 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 164 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 125 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 288 CYS cc_start: 0.8344 (t) cc_final: 0.8072 (t) REVERT: B 454 PHE cc_start: 0.8501 (m-10) cc_final: 0.8124 (m-80) REVERT: B 466 ILE cc_start: 0.9333 (mt) cc_final: 0.9069 (tt) REVERT: A 122 TYR cc_start: 0.6968 (OUTLIER) cc_final: 0.6556 (t80) REVERT: A 332 ASP cc_start: 0.8358 (t0) cc_final: 0.8118 (t0) REVERT: A 433 LEU cc_start: 0.9129 (mm) cc_final: 0.8830 (mm) REVERT: A 454 PHE cc_start: 0.8573 (m-10) cc_final: 0.8350 (m-80) outliers start: 39 outliers final: 26 residues processed: 150 average time/residue: 0.1323 time to fit residues: 28.8894 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 : 0.680 ------------------------------------------------------------------------------- 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 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 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 356 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 39 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 3 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 chunk 40 optimal weight: 1.9990 chunk 13 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: ** 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 = 0.4173 r_free = 0.4173 target = 0.096356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.079924 restraints weight = 31298.691| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 4.92 r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.4462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 6646 Z= 0.244 Angle : 0.759 12.841 9052 Z= 0.357 Chirality : 0.043 0.316 1118 Planarity : 0.004 0.043 1094 Dihedral : 4.421 30.223 910 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 7.31 % Allowed : 18.05 % Favored : 74.64 % 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: 1.38 (0.30), residues: 860 helix: 1.68 (0.20), residues: 678 sheet: None (None), residues: 0 loop : -2.08 (0.48), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 377 HIS 0.002 0.001 HIS A 169 PHE 0.010 0.001 PHE A 121 TYR 0.013 0.001 TYR B 485 ARG 0.004 0.000 ARG A 156 *********************** 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 172 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 121 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 214 GLU cc_start: 0.8588 (tt0) cc_final: 0.7661 (tp30) REVERT: B 454 PHE cc_start: 0.8525 (m-10) cc_final: 0.8124 (m-80) REVERT: B 466 ILE cc_start: 0.9360 (mt) cc_final: 0.9013 (tt) REVERT: A 122 TYR cc_start: 0.6920 (OUTLIER) cc_final: 0.6547 (t80) REVERT: A 332 ASP cc_start: 0.8419 (t0) cc_final: 0.8168 (t0) REVERT: A 433 LEU cc_start: 0.9146 (mm) cc_final: 0.8846 (mm) REVERT: A 454 PHE cc_start: 0.8570 (m-10) cc_final: 0.8352 (m-80) outliers start: 51 outliers final: 35 residues processed: 153 average time/residue: 0.1361 time to fit residues: 30.0075 Evaluate side-chains 151 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 115 time to evaluate : 0.756 ------------------------------------------------------------------------------- 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 343 LEU 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 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 253 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 356 PHE Chi-restraints excluded: chain A residue 364 LEU 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: 0.5980 chunk 51 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 42 optimal weight: 20.0000 chunk 26 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4190 r_free = 0.4190 target = 0.097215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.082924 restraints weight = 31456.719| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 4.32 r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.4628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6646 Z= 0.183 Angle : 0.775 12.723 9052 Z= 0.356 Chirality : 0.042 0.304 1118 Planarity : 0.004 0.041 1094 Dihedral : 4.391 29.438 910 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 5.30 % Allowed : 21.06 % 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: 1.17 (0.30), residues: 860 helix: 1.55 (0.20), residues: 676 sheet: None (None), residues: 0 loop : -2.21 (0.48), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 377 HIS 0.002 0.001 HIS B 477 PHE 0.014 0.001 PHE B 358 TYR 0.017 0.002 TYR A 260 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 155 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 118 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 214 GLU cc_start: 0.8532 (tt0) cc_final: 0.7685 (tp30) REVERT: B 454 PHE cc_start: 0.8463 (m-10) cc_final: 0.8070 (m-80) REVERT: B 485 TYR cc_start: 0.8550 (m-80) cc_final: 0.8209 (m-80) REVERT: A 122 TYR cc_start: 0.6856 (OUTLIER) cc_final: 0.6505 (t80) REVERT: A 332 ASP cc_start: 0.8281 (t0) cc_final: 0.8002 (t0) REVERT: A 433 LEU cc_start: 0.9179 (mm) cc_final: 0.8867 (mm) REVERT: A 454 PHE cc_start: 0.8492 (m-10) cc_final: 0.8179 (m-80) outliers start: 37 outliers final: 27 residues processed: 141 average time/residue: 0.1472 time to fit residues: 29.2803 Evaluate side-chains 135 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 107 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 VAL 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 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 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 289 LEU Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 406 GLU 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: 8.9990 chunk 22 optimal weight: 8.9990 chunk 4 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 41 optimal weight: 10.0000 chunk 85 optimal weight: 0.8980 chunk 16 optimal weight: 10.0000 chunk 80 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 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 = 0.4187 r_free = 0.4187 target = 0.096709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.080860 restraints weight = 29845.524| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 4.88 r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.4796 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= 0.187 Angle : 0.763 12.893 9052 Z= 0.356 Chirality : 0.042 0.287 1118 Planarity : 0.004 0.041 1094 Dihedral : 4.396 30.133 910 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 5.73 % Allowed : 21.35 % 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: 1.25 (0.30), residues: 860 helix: 1.62 (0.20), residues: 676 sheet: None (None), residues: 0 loop : -2.22 (0.48), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 377 HIS 0.001 0.000 HIS A 169 PHE 0.014 0.001 PHE B 451 TYR 0.014 0.001 TYR B 260 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: 40 poor density : 115 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 214 GLU cc_start: 0.8629 (tt0) cc_final: 0.7835 (tp30) REVERT: B 377 TRP cc_start: 0.7135 (t-100) cc_final: 0.6848 (t-100) REVERT: B 454 PHE cc_start: 0.8469 (m-10) cc_final: 0.8061 (m-80) REVERT: A 122 TYR cc_start: 0.7256 (OUTLIER) cc_final: 0.6783 (t80) REVERT: A 181 SER cc_start: 0.7522 (OUTLIER) cc_final: 0.7250 (t) REVERT: A 433 LEU cc_start: 0.9232 (mm) cc_final: 0.8896 (mm) REVERT: A 454 PHE cc_start: 0.8744 (m-10) cc_final: 0.8330 (m-80) REVERT: A 490 LEU cc_start: 0.9019 (mt) cc_final: 0.8815 (mt) outliers start: 40 outliers final: 26 residues processed: 139 average time/residue: 0.1403 time to fit residues: 28.1850 Evaluate side-chains 136 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 108 time to evaluate : 0.720 ------------------------------------------------------------------------------- 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 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 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 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 289 LEU Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 406 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 36 optimal weight: 7.9990 chunk 69 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 42 optimal weight: 8.9990 chunk 26 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 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 = 0.4182 r_free = 0.4182 target = 0.096444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.082063 restraints weight = 30780.520| |-----------------------------------------------------------------------------| r_work (start): 0.3883 rms_B_bonded: 4.38 r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.4944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6646 Z= 0.193 Angle : 0.781 12.708 9052 Z= 0.364 Chirality : 0.042 0.285 1118 Planarity : 0.004 0.042 1094 Dihedral : 4.423 30.373 910 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 4.73 % Allowed : 23.50 % Favored : 71.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.59 (0.20), residues: 676 sheet: None (None), residues: 0 loop : -2.39 (0.47), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 392 HIS 0.002 0.001 HIS A 169 PHE 0.020 0.001 PHE A 322 TYR 0.016 0.001 TYR A 260 ARG 0.003 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 144 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 111 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 214 GLU cc_start: 0.8596 (tt0) cc_final: 0.7840 (tp30) REVERT: B 377 TRP cc_start: 0.6711 (t-100) cc_final: 0.6419 (t-100) REVERT: B 454 PHE cc_start: 0.8456 (m-10) cc_final: 0.8042 (m-80) REVERT: A 122 TYR cc_start: 0.6819 (OUTLIER) cc_final: 0.6487 (t80) REVERT: A 181 SER cc_start: 0.7584 (OUTLIER) cc_final: 0.7360 (t) REVERT: A 433 LEU cc_start: 0.9108 (mm) cc_final: 0.8791 (mm) REVERT: A 454 PHE cc_start: 0.8453 (m-10) cc_final: 0.8152 (m-80) outliers start: 33 outliers final: 25 residues processed: 129 average time/residue: 0.1325 time to fit residues: 24.6803 Evaluate side-chains 132 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 105 time to evaluate : 0.696 ------------------------------------------------------------------------------- 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 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 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 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 280 LEU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 406 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 13 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 19 optimal weight: 0.0020 chunk 58 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 35 optimal weight: 7.9990 chunk 8 optimal weight: 10.0000 chunk 43 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 39 optimal weight: 9.9990 overall best weight: 0.7190 ------------------------------------------------------------------------------- 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 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 231 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.096982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.082956 restraints weight = 31411.017| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 4.27 r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.5041 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 : 0.772 12.561 9052 Z= 0.361 Chirality : 0.041 0.190 1118 Planarity : 0.004 0.042 1094 Dihedral : 4.374 29.809 910 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 4.87 % Allowed : 23.21 % Favored : 71.92 % 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: 1.14 (0.30), residues: 860 helix: 1.58 (0.20), residues: 676 sheet: None (None), residues: 0 loop : -2.43 (0.47), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 392 HIS 0.001 0.000 HIS A 169 PHE 0.020 0.001 PHE A 322 TYR 0.017 0.001 TYR A 260 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: 34 poor density : 116 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 MET cc_start: 0.8296 (mtm) cc_final: 0.8026 (mpp) REVERT: B 145 LEU cc_start: 0.8628 (mp) cc_final: 0.8410 (mp) REVERT: B 214 GLU cc_start: 0.8593 (tt0) cc_final: 0.7868 (mm-30) REVERT: B 377 TRP cc_start: 0.6666 (t-100) cc_final: 0.6388 (t-100) REVERT: B 454 PHE cc_start: 0.8424 (m-10) cc_final: 0.8008 (m-80) REVERT: A 122 TYR cc_start: 0.6791 (OUTLIER) cc_final: 0.6456 (t80) REVERT: A 181 SER cc_start: 0.7538 (OUTLIER) cc_final: 0.7311 (t) REVERT: A 291 MET cc_start: 0.7433 (ppp) cc_final: 0.5787 (mmp) REVERT: A 433 LEU cc_start: 0.9114 (mm) cc_final: 0.8781 (mm) REVERT: A 454 PHE cc_start: 0.8384 (m-10) cc_final: 0.8089 (m-80) outliers start: 34 outliers final: 25 residues processed: 137 average time/residue: 0.1403 time to fit residues: 27.5158 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 : 0.752 ------------------------------------------------------------------------------- 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 444 PHE 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 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 181 SER Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 406 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 28 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 32 optimal weight: 0.3980 chunk 8 optimal weight: 0.0770 chunk 82 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 overall best weight: 0.6338 ------------------------------------------------------------------------------- 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 463 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 = 0.4196 r_free = 0.4196 target = 0.097372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.083247 restraints weight = 31227.044| |-----------------------------------------------------------------------------| r_work (start): 0.3898 rms_B_bonded: 4.28 r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.5123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6646 Z= 0.179 Angle : 0.790 12.393 9052 Z= 0.370 Chirality : 0.041 0.202 1118 Planarity : 0.004 0.042 1094 Dihedral : 4.388 30.199 910 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 4.44 % Allowed : 24.50 % 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: 1.12 (0.30), residues: 860 helix: 1.57 (0.20), residues: 674 sheet: None (None), residues: 0 loop : -2.43 (0.46), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 392 HIS 0.001 0.000 HIS A 169 PHE 0.020 0.001 PHE A 322 TYR 0.019 0.001 TYR A 260 ARG 0.004 0.000 ARG A 431 *********************** 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 145 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 114 time to evaluate : 0.766 Fit side-chains revert: symmetry clash REVERT: B 145 LEU cc_start: 0.8612 (mp) cc_final: 0.8400 (mp) REVERT: B 214 GLU cc_start: 0.8582 (tt0) cc_final: 0.7866 (mm-30) REVERT: B 377 TRP cc_start: 0.6589 (t-100) cc_final: 0.6293 (t-100) REVERT: B 454 PHE cc_start: 0.8390 (m-10) cc_final: 0.8026 (m-80) REVERT: A 122 TYR cc_start: 0.6734 (OUTLIER) cc_final: 0.6406 (t80) REVERT: A 181 SER cc_start: 0.7538 (OUTLIER) cc_final: 0.7306 (t) REVERT: A 291 MET cc_start: 0.7063 (ppp) cc_final: 0.5580 (mmp) REVERT: A 433 LEU cc_start: 0.9094 (mm) cc_final: 0.8771 (mm) REVERT: A 454 PHE cc_start: 0.8358 (m-10) cc_final: 0.8144 (m-80) outliers start: 31 outliers final: 26 residues processed: 133 average time/residue: 0.1497 time to fit residues: 29.0496 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 : 0.736 ------------------------------------------------------------------------------- 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 444 PHE 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 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 181 SER Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 364 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 9 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 35 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 85 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 chunk 81 optimal weight: 0.7980 chunk 67 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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 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 = 0.4164 r_free = 0.4164 target = 0.095091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.080034 restraints weight = 32144.191| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 4.44 r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.5317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6646 Z= 0.280 Angle : 0.839 13.502 9052 Z= 0.407 Chirality : 0.044 0.234 1118 Planarity : 0.004 0.044 1094 Dihedral : 4.579 31.115 910 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 17.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 4.30 % Allowed : 24.79 % Favored : 70.92 % 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: 1.02 (0.30), residues: 860 helix: 1.47 (0.20), residues: 676 sheet: None (None), residues: 0 loop : -2.37 (0.48), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 392 HIS 0.003 0.001 HIS A 169 PHE 0.018 0.002 PHE A 322 TYR 0.021 0.002 TYR A 260 ARG 0.006 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: 30 poor density : 108 time to evaluate : 0.752 Fit side-chains revert: symmetry clash REVERT: B 148 MET cc_start: 0.7118 (mtp) cc_final: 0.6378 (mtp) REVERT: B 214 GLU cc_start: 0.8720 (tt0) cc_final: 0.8007 (tp30) REVERT: B 377 TRP cc_start: 0.6881 (t-100) cc_final: 0.6365 (t-100) REVERT: B 454 PHE cc_start: 0.8475 (m-10) cc_final: 0.8113 (m-80) REVERT: A 122 TYR cc_start: 0.6889 (OUTLIER) cc_final: 0.6563 (t80) REVERT: A 181 SER cc_start: 0.7637 (OUTLIER) cc_final: 0.7389 (t) REVERT: A 291 MET cc_start: 0.7391 (ppp) cc_final: 0.5935 (mmp) REVERT: A 433 LEU cc_start: 0.9126 (mm) cc_final: 0.8773 (mm) REVERT: A 454 PHE cc_start: 0.8476 (m-10) cc_final: 0.8264 (m-80) outliers start: 30 outliers final: 28 residues processed: 126 average time/residue: 0.1276 time to fit residues: 23.7886 Evaluate side-chains 136 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 106 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 153 PHE 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 444 PHE 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 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 181 SER Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 364 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 85 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 35 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 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 = 0.096859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.082248 restraints weight = 32172.740| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 4.26 r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.5334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 6646 Z= 0.215 Angle : 0.866 18.589 9052 Z= 0.405 Chirality : 0.043 0.267 1118 Planarity : 0.004 0.043 1094 Dihedral : 4.540 30.010 910 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 4.15 % Allowed : 25.79 % Favored : 70.06 % 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: 1.10 (0.30), residues: 860 helix: 1.55 (0.20), residues: 674 sheet: None (None), residues: 0 loop : -2.40 (0.47), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 232 HIS 0.001 0.000 HIS A 169 PHE 0.015 0.001 PHE A 131 TYR 0.020 0.001 TYR A 260 ARG 0.004 0.000 ARG A 431 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3190.23 seconds wall clock time: 57 minutes 18.65 seconds (3438.65 seconds total)