Starting phenix.real_space_refine on Tue Sep 24 01:39:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p1j_13162/09_2024/7p1j_13162.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p1j_13162/09_2024/7p1j_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p1j_13162/09_2024/7p1j_13162.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p1j_13162/09_2024/7p1j_13162.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p1j_13162/09_2024/7p1j_13162.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p1j_13162/09_2024/7p1j_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 4.55, per 1000 atoms: 0.70 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: 1.58 Conformation dependent library (CDL) restraints added in 974.6 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: 0.58 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: 1.75 Time building geometry restraints manager: 1.87 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: 0.00 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: 0.960 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.660 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.030 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.040 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 16 poor density : 231 time to evaluate : 0.728 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: 0.1509 time to fit residues: 50.0169 Evaluate side-chains 133 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 130 time to evaluate : 0.740 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 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 fitting. rotamer outliers: 36 poor density : 142 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 424 LEU cc_start: 0.9081 (mt) cc_final: 0.8844 (mp) REVERT: B 440 CYS cc_start: 0.7038 (p) cc_final: 0.6735 (m) REVERT: B 454 PHE cc_start: 0.8558 (m-10) cc_final: 0.8172 (m-80) REVERT: B 466 ILE cc_start: 0.9347 (mt) cc_final: 0.9076 (tt) REVERT: A 122 TYR cc_start: 0.6864 (OUTLIER) cc_final: 0.6499 (t80) REVERT: A 326 PHE cc_start: 0.7421 (m-80) cc_final: 0.7128 (m-80) REVERT: A 332 ASP cc_start: 0.8270 (t0) cc_final: 0.8058 (t0) REVERT: A 454 PHE cc_start: 0.8553 (m-10) cc_final: 0.8312 (m-80) REVERT: A 490 LEU cc_start: 0.8740 (mt) cc_final: 0.8354 (mt) outliers start: 36 outliers final: 24 residues processed: 167 average time/residue: 0.1270 time to fit residues: 30.5924 Evaluate side-chains 143 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 118 time to evaluate : 0.692 ------------------------------------------------------------------------------- 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 43 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 78 optimal weight: 10.0000 chunk 84 optimal weight: 0.0770 chunk 69 optimal weight: 0.5980 chunk 77 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 overall best weight: 0.8540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.4064 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= 0.191 Angle : 0.807 16.691 9052 Z= 0.362 Chirality : 0.044 0.264 1118 Planarity : 0.004 0.041 1094 Dihedral : 4.265 29.617 910 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 5.01 % Allowed : 18.77 % Favored : 76.22 % 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: 1.52 (0.30), residues: 860 helix: 1.89 (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 0.021 0.001 PHE A 322 TYR 0.011 0.001 TYR B 485 ARG 0.002 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 163 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 128 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 288 CYS cc_start: 0.8232 (t) cc_final: 0.8007 (t) REVERT: B 440 CYS cc_start: 0.7221 (p) cc_final: 0.6994 (m) REVERT: B 454 PHE cc_start: 0.8465 (m-10) cc_final: 0.8063 (m-80) REVERT: B 466 ILE cc_start: 0.9309 (mt) cc_final: 0.9038 (tt) REVERT: A 122 TYR cc_start: 0.6776 (OUTLIER) cc_final: 0.6425 (t80) REVERT: A 332 ASP cc_start: 0.8292 (t0) cc_final: 0.8042 (t0) REVERT: A 454 PHE cc_start: 0.8521 (m-10) cc_final: 0.8282 (m-80) outliers start: 35 outliers final: 22 residues processed: 150 average time/residue: 0.1309 time to fit residues: 28.3410 Evaluate side-chains 141 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 118 time to evaluate : 0.760 ------------------------------------------------------------------------------- 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 77 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 37 optimal weight: 0.3980 chunk 52 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 41 optimal weight: 8.9990 chunk 74 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.4364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 6646 Z= 0.228 Angle : 0.742 13.199 9052 Z= 0.348 Chirality : 0.041 0.278 1118 Planarity : 0.004 0.042 1094 Dihedral : 4.339 30.334 910 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 7.02 % Allowed : 18.34 % 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: 1.37 (0.30), residues: 860 helix: 1.77 (0.20), residues: 670 sheet: None (None), residues: 0 loop : -2.34 (0.46), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 377 HIS 0.002 0.001 HIS A 169 PHE 0.024 0.001 PHE A 322 TYR 0.012 0.001 TYR B 485 ARG 0.003 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 175 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 126 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 214 GLU cc_start: 0.8315 (tt0) cc_final: 0.7549 (tp30) REVERT: B 288 CYS cc_start: 0.8302 (t) cc_final: 0.8087 (t) REVERT: B 440 CYS cc_start: 0.7240 (p) cc_final: 0.7026 (m) REVERT: B 454 PHE cc_start: 0.8461 (m-10) cc_final: 0.8041 (m-80) REVERT: B 466 ILE cc_start: 0.9305 (mt) cc_final: 0.8949 (tt) REVERT: A 122 TYR cc_start: 0.6785 (OUTLIER) cc_final: 0.6447 (t80) REVERT: A 131 PHE cc_start: 0.7738 (m-10) cc_final: 0.7535 (m-10) REVERT: A 332 ASP cc_start: 0.8361 (t0) cc_final: 0.8105 (t0) REVERT: A 433 LEU cc_start: 0.9089 (mm) cc_final: 0.8832 (mm) REVERT: A 454 PHE cc_start: 0.8531 (m-10) cc_final: 0.8294 (m-80) outliers start: 49 outliers final: 34 residues processed: 155 average time/residue: 0.1284 time to fit residues: 28.7404 Evaluate side-chains 152 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 117 time to evaluate : 0.658 ------------------------------------------------------------------------------- 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 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 303 LEU 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 69 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 61 optimal weight: 0.0770 chunk 34 optimal weight: 6.9990 chunk 70 optimal weight: 0.9980 chunk 57 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 42 optimal weight: 20.0000 chunk 74 optimal weight: 0.8980 chunk 20 optimal weight: 6.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- 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** ** B 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 157 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.4558 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= 0.179 Angle : 0.749 11.959 9052 Z= 0.346 Chirality : 0.041 0.287 1118 Planarity : 0.004 0.041 1094 Dihedral : 4.345 29.853 910 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 6.02 % Allowed : 20.06 % 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: 1.22 (0.30), residues: 860 helix: 1.61 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -2.40 (0.48), residues: 180 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 0.011 0.001 PHE A 285 TYR 0.043 0.002 TYR B 485 ARG 0.004 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 164 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 122 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 214 GLU cc_start: 0.8311 (tt0) cc_final: 0.7697 (mm-30) REVERT: B 377 TRP cc_start: 0.6574 (t-100) cc_final: 0.6254 (t-100) REVERT: B 454 PHE cc_start: 0.8414 (m-10) cc_final: 0.7992 (m-80) REVERT: B 485 TYR cc_start: 0.8656 (m-80) cc_final: 0.8285 (m-80) REVERT: A 122 TYR cc_start: 0.6778 (OUTLIER) cc_final: 0.6437 (t80) REVERT: A 181 SER cc_start: 0.7405 (OUTLIER) cc_final: 0.7168 (t) REVERT: A 235 MET cc_start: 0.7056 (mtt) cc_final: 0.6827 (mtt) REVERT: A 332 ASP cc_start: 0.8327 (t0) cc_final: 0.7949 (t0) REVERT: A 433 LEU cc_start: 0.9076 (mm) cc_final: 0.8852 (mm) REVERT: A 454 PHE cc_start: 0.8497 (m-10) cc_final: 0.8162 (m-80) REVERT: A 490 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8888 (mt) outliers start: 42 outliers final: 24 residues processed: 149 average time/residue: 0.1413 time to fit residues: 29.9360 Evaluate side-chains 136 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 109 time to evaluate : 0.692 ------------------------------------------------------------------------------- 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 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 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 27 optimal weight: 10.0000 chunk 74 optimal weight: 0.6980 chunk 16 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 38 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 80 optimal weight: 0.0270 overall best weight: 0.8840 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.4741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6646 Z= 0.181 Angle : 0.758 12.854 9052 Z= 0.353 Chirality : 0.041 0.155 1118 Planarity : 0.004 0.041 1094 Dihedral : 4.356 30.025 910 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 5.30 % Allowed : 21.20 % 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: 1.20 (0.30), residues: 860 helix: 1.61 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -2.43 (0.48), residues: 180 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 0.014 0.001 PHE B 451 TYR 0.044 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 153 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 116 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 214 GLU cc_start: 0.8311 (tt0) cc_final: 0.7698 (mm-30) REVERT: B 454 PHE cc_start: 0.8410 (m-10) cc_final: 0.7984 (m-80) REVERT: A 122 TYR cc_start: 0.6772 (OUTLIER) cc_final: 0.6434 (t80) REVERT: A 181 SER cc_start: 0.7401 (OUTLIER) cc_final: 0.7169 (t) REVERT: A 235 MET cc_start: 0.6949 (mtt) cc_final: 0.6362 (mtt) REVERT: A 433 LEU cc_start: 0.9067 (mm) cc_final: 0.8800 (mm) REVERT: A 454 PHE cc_start: 0.8460 (m-10) cc_final: 0.8135 (m-80) REVERT: A 490 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8713 (mt) outliers start: 37 outliers final: 25 residues processed: 140 average time/residue: 0.1361 time to fit residues: 27.3789 Evaluate side-chains 138 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 110 time to evaluate : 0.817 ------------------------------------------------------------------------------- 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 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 364 LEU Chi-restraints excluded: chain A residue 406 GLU 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 9 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 70 optimal weight: 8.9990 chunk 46 optimal weight: 0.0980 chunk 82 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 49 optimal weight: 0.0980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.4869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6646 Z= 0.172 Angle : 0.775 12.399 9052 Z= 0.357 Chirality : 0.041 0.266 1118 Planarity : 0.004 0.041 1094 Dihedral : 4.330 29.922 910 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 4.15 % Allowed : 23.50 % Favored : 72.35 % 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: 1.16 (0.30), residues: 860 helix: 1.58 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -2.47 (0.48), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 377 HIS 0.001 0.000 HIS A 169 PHE 0.012 0.001 PHE B 358 TYR 0.044 0.002 TYR B 485 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 141 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 112 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 MET cc_start: 0.8260 (mtm) cc_final: 0.7995 (mpp) REVERT: B 165 ILE cc_start: 0.8436 (OUTLIER) cc_final: 0.8210 (mp) REVERT: B 214 GLU cc_start: 0.8299 (tt0) cc_final: 0.7544 (tp30) REVERT: B 454 PHE cc_start: 0.8387 (m-10) cc_final: 0.7943 (m-80) REVERT: A 122 TYR cc_start: 0.6753 (OUTLIER) cc_final: 0.6404 (t80) REVERT: A 235 MET cc_start: 0.7192 (mtt) cc_final: 0.6599 (mtt) REVERT: A 433 LEU cc_start: 0.9071 (mm) cc_final: 0.8825 (mm) REVERT: A 454 PHE cc_start: 0.8430 (m-10) cc_final: 0.8095 (m-80) REVERT: A 490 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8727 (mt) outliers start: 29 outliers final: 21 residues processed: 130 average time/residue: 0.1292 time to fit residues: 24.4544 Evaluate side-chains 131 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 107 time to evaluate : 0.749 ------------------------------------------------------------------------------- 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 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 364 LEU Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 490 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 24 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 chunk 52 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 75 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 77 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** ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.4972 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= 0.178 Angle : 0.764 11.522 9052 Z= 0.355 Chirality : 0.041 0.179 1118 Planarity : 0.004 0.041 1094 Dihedral : 4.313 30.314 910 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 5.16 % Allowed : 23.07 % 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: 1.61 (0.20), residues: 678 sheet: None (None), residues: 0 loop : -2.48 (0.47), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 377 HIS 0.001 0.000 HIS A 169 PHE 0.020 0.001 PHE A 322 TYR 0.041 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 148 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 112 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 214 GLU cc_start: 0.8311 (tt0) cc_final: 0.7546 (tp30) REVERT: B 454 PHE cc_start: 0.8398 (m-10) cc_final: 0.7953 (m-80) REVERT: A 122 TYR cc_start: 0.6773 (OUTLIER) cc_final: 0.6441 (t80) REVERT: A 181 SER cc_start: 0.7416 (OUTLIER) cc_final: 0.7163 (t) REVERT: A 235 MET cc_start: 0.7132 (mtt) cc_final: 0.6657 (mtt) REVERT: A 433 LEU cc_start: 0.9051 (mm) cc_final: 0.8770 (mm) REVERT: A 454 PHE cc_start: 0.8429 (m-10) cc_final: 0.8090 (m-80) REVERT: A 490 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8716 (mt) outliers start: 36 outliers final: 25 residues processed: 134 average time/residue: 0.1273 time to fit residues: 24.8547 Evaluate side-chains 136 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 108 time to evaluate : 0.717 ------------------------------------------------------------------------------- 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 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 287 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 79 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 33 optimal weight: 0.0970 chunk 60 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 69 optimal weight: 0.9990 chunk 73 optimal weight: 0.5980 chunk 76 optimal weight: 8.9990 chunk 50 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 49 optimal weight: 20.0000 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.5047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6646 Z= 0.184 Angle : 0.796 13.656 9052 Z= 0.368 Chirality : 0.041 0.183 1118 Planarity : 0.004 0.041 1094 Dihedral : 4.333 30.082 910 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 3.72 % Allowed : 25.07 % Favored : 71.20 % 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: 678 sheet: None (None), residues: 0 loop : -2.48 (0.47), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 377 HIS 0.001 0.000 HIS A 169 PHE 0.019 0.001 PHE A 322 TYR 0.041 0.002 TYR B 485 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 140 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 114 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 214 GLU cc_start: 0.8317 (tt0) cc_final: 0.7552 (tp30) REVERT: B 454 PHE cc_start: 0.8395 (m-10) cc_final: 0.7949 (m-80) REVERT: A 122 TYR cc_start: 0.6794 (OUTLIER) cc_final: 0.6464 (t80) REVERT: A 181 SER cc_start: 0.7401 (OUTLIER) cc_final: 0.7154 (t) REVERT: A 235 MET cc_start: 0.7198 (mtt) cc_final: 0.6726 (mtt) REVERT: A 291 MET cc_start: 0.7216 (ppp) cc_final: 0.5806 (mmp) REVERT: A 433 LEU cc_start: 0.9043 (mm) cc_final: 0.8769 (mm) REVERT: A 454 PHE cc_start: 0.8396 (m-10) cc_final: 0.8064 (m-80) outliers start: 26 outliers final: 22 residues processed: 128 average time/residue: 0.1377 time to fit residues: 26.3475 Evaluate side-chains 134 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 110 time to evaluate : 0.763 ------------------------------------------------------------------------------- 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 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 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 364 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 38 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 85 optimal weight: 0.5980 chunk 78 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 41 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 477 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.5160 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= 0.182 Angle : 0.790 12.914 9052 Z= 0.366 Chirality : 0.041 0.180 1118 Planarity : 0.004 0.042 1094 Dihedral : 4.332 30.100 910 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 4.01 % Allowed : 25.21 % Favored : 70.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 678 sheet: None (None), residues: 0 loop : -2.42 (0.48), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP B 377 HIS 0.001 0.000 HIS A 169 PHE 0.022 0.001 PHE A 131 TYR 0.040 0.002 TYR B 485 ARG 0.004 0.000 ARG A 431 ********************** 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 140 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 112 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 214 GLU cc_start: 0.8332 (tt0) cc_final: 0.7562 (tp30) REVERT: B 454 PHE cc_start: 0.8405 (m-10) cc_final: 0.8010 (m-80) REVERT: A 122 TYR cc_start: 0.6784 (OUTLIER) cc_final: 0.6457 (t80) REVERT: A 181 SER cc_start: 0.7424 (OUTLIER) cc_final: 0.7167 (t) REVERT: A 235 MET cc_start: 0.7208 (mtt) cc_final: 0.6728 (mtt) REVERT: A 291 MET cc_start: 0.7183 (ppp) cc_final: 0.5836 (mmp) REVERT: A 433 LEU cc_start: 0.9053 (mm) cc_final: 0.8752 (mm) REVERT: A 454 PHE cc_start: 0.8349 (m-10) cc_final: 0.8103 (m-80) REVERT: A 487 MET cc_start: 0.8368 (tmm) cc_final: 0.8156 (tmm) outliers start: 28 outliers final: 25 residues processed: 129 average time/residue: 0.1281 time to fit residues: 24.1375 Evaluate side-chains 136 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 109 time to evaluate : 0.742 ------------------------------------------------------------------------------- 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 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 287 THR 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 62 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 18 optimal weight: 0.0670 chunk 68 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 70 optimal weight: 0.0060 chunk 8 optimal weight: 0.0370 chunk 12 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 49 optimal weight: 0.0000 overall best weight: 0.2216 ------------------------------------------------------------------------------- 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 = 0.4221 r_free = 0.4221 target = 0.098991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.084649 restraints weight = 30635.159| |-----------------------------------------------------------------------------| r_work (start): 0.3926 rms_B_bonded: 4.51 r_work (final): 0.3926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 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 0.044 6646 Z= 0.169 Angle : 0.797 12.927 9052 Z= 0.364 Chirality : 0.041 0.190 1118 Planarity : 0.004 0.041 1094 Dihedral : 4.302 29.373 910 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 3.44 % Allowed : 26.07 % Favored : 70.49 % 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: 1.13 (0.30), residues: 860 helix: 1.55 (0.20), residues: 678 sheet: None (None), residues: 0 loop : -2.38 (0.48), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 377 HIS 0.001 0.000 HIS A 477 PHE 0.023 0.001 PHE A 131 TYR 0.041 0.001 TYR B 485 ARG 0.003 0.000 ARG A 431 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1518.44 seconds wall clock time: 27 minutes 52.09 seconds (1672.09 seconds total)