Starting phenix.real_space_refine on Mon Mar 11 01:15:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p1j_13162/03_2024/7p1j_13162.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p1j_13162/03_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_13162/03_2024/7p1j_13162.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p1j_13162/03_2024/7p1j_13162.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p1j_13162/03_2024/7p1j_13162.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p1j_13162/03_2024/7p1j_13162.pdb" } 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 Residue "B PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 494": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 4.02, per 1000 atoms: 0.62 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.99 Conformation dependent library (CDL) restraints added in 1.5 seconds 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1544 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 0 sheets defined 83.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 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: 1.91 Time building geometry restraints manager: 3.14 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: 100.41 - 107.13: 208 107.13 - 113.85: 3910 113.85 - 120.57: 2642 120.57 - 127.29: 2214 127.29 - 134.01: 78 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 2.520 nonbonded pdb=" O PHE A 444 " pdb=" NZ LYS A 449 " model vdw 2.314 2.520 nonbonded pdb=" O PHE B 444 " pdb=" NZ LYS B 449 " model vdw 2.315 2.520 nonbonded pdb=" OG SER B 106 " pdb=" OE1 GLU B 107 " model vdw 2.322 2.440 nonbonded pdb=" O PHE B 153 " pdb=" ND2 ASN B 157 " model vdw 2.372 2.520 ... (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 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: 1.060 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: 3.210 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 22.240 Find NCS groups from input model: 0.370 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: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.950 ------------------------------------------------------------------------------- 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 : 0.803 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: 0.1550 time to fit residues: 51.5025 Evaluate side-chains 133 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 130 time to evaluate : 0.754 ------------------------------------------------------------------------------- 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: 3.9990 chunk 65 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 43 optimal weight: 0.2980 chunk 34 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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: 0.7334 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6646 Z= 0.226 Angle : 0.787 11.430 9052 Z= 0.367 Chirality : 0.044 0.368 1118 Planarity : 0.005 0.075 1094 Dihedral : 3.826 26.880 910 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 5.44 % Allowed : 19.34 % Favored : 75.21 % 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: 2.00 (0.30), residues: 860 helix: 2.23 (0.20), residues: 668 sheet: None (None), residues: 0 loop : -2.12 (0.48), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 377 HIS 0.001 0.000 HIS B 169 PHE 0.013 0.002 PHE B 358 TYR 0.009 0.001 TYR B 485 ARG 0.012 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 183 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 145 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 322 PHE cc_start: 0.8174 (m-10) cc_final: 0.7900 (m-80) REVERT: B 424 LEU cc_start: 0.9069 (mt) cc_final: 0.8843 (mp) REVERT: B 440 CYS cc_start: 0.7083 (p) cc_final: 0.6823 (m) REVERT: B 454 PHE cc_start: 0.8534 (m-10) cc_final: 0.8150 (m-80) REVERT: B 466 ILE cc_start: 0.9345 (mt) cc_final: 0.9071 (tt) REVERT: A 326 PHE cc_start: 0.7351 (m-80) cc_final: 0.7045 (m-80) REVERT: A 454 PHE cc_start: 0.8520 (m-10) cc_final: 0.8271 (m-80) REVERT: A 490 LEU cc_start: 0.8553 (mt) cc_final: 0.8072 (mt) outliers start: 38 outliers final: 26 residues processed: 172 average time/residue: 0.1336 time to fit residues: 32.7733 Evaluate side-chains 148 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 122 time to evaluate : 0.761 ------------------------------------------------------------------------------- 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 330 ASP Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain A residue 86 VAL 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 303 LEU Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain A residue 356 PHE Chi-restraints excluded: chain A residue 424 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 43 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 78 optimal weight: 10.0000 chunk 84 optimal weight: 9.9990 chunk 69 optimal weight: 0.6980 chunk 77 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7368 moved from start: 0.4105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6646 Z= 0.217 Angle : 0.791 15.032 9052 Z= 0.359 Chirality : 0.043 0.284 1118 Planarity : 0.004 0.040 1094 Dihedral : 4.065 25.980 910 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 17.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 5.30 % Allowed : 19.63 % Favored : 75.07 % 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: 1.62 (0.30), residues: 860 helix: 1.97 (0.20), residues: 668 sheet: None (None), residues: 0 loop : -2.28 (0.47), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 377 HIS 0.002 0.001 HIS A 169 PHE 0.018 0.001 PHE A 322 TYR 0.011 0.001 TYR B 485 ARG 0.003 0.000 ARG B 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 166 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 129 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 214 GLU cc_start: 0.8184 (tt0) cc_final: 0.7406 (tp30) REVERT: B 288 CYS cc_start: 0.8265 (t) cc_final: 0.7996 (t) REVERT: B 454 PHE cc_start: 0.8474 (m-10) cc_final: 0.8075 (m-80) REVERT: B 466 ILE cc_start: 0.9333 (mt) cc_final: 0.9051 (tt) REVERT: A 122 TYR cc_start: 0.6796 (OUTLIER) cc_final: 0.6442 (t80) REVERT: A 454 PHE cc_start: 0.8537 (m-10) cc_final: 0.8303 (m-80) outliers start: 37 outliers final: 27 residues processed: 152 average time/residue: 0.1344 time to fit residues: 29.3355 Evaluate side-chains 144 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 116 time to evaluate : 0.670 ------------------------------------------------------------------------------- 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 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 330 ASP 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 130 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 269 LEU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain A residue 356 PHE Chi-restraints excluded: chain A residue 383 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 77 optimal weight: 6.9990 chunk 58 optimal weight: 0.9980 chunk 40 optimal weight: 8.9990 chunk 8 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 78 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 22 optimal weight: 7.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7391 moved from start: 0.4414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6646 Z= 0.209 Angle : 0.736 15.550 9052 Z= 0.345 Chirality : 0.042 0.285 1118 Planarity : 0.004 0.039 1094 Dihedral : 4.157 25.747 910 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 6.30 % Allowed : 19.48 % Favored : 74.21 % 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: 1.70 (0.20), residues: 682 sheet: None (None), residues: 0 loop : -2.28 (0.49), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 377 HIS 0.002 0.001 HIS A 169 PHE 0.012 0.001 PHE B 358 TYR 0.012 0.001 TYR B 485 ARG 0.002 0.000 ARG A 475 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 125 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 214 GLU cc_start: 0.8256 (tt0) cc_final: 0.7452 (tp30) REVERT: B 288 CYS cc_start: 0.8284 (t) cc_final: 0.8061 (t) REVERT: B 454 PHE cc_start: 0.8449 (m-10) cc_final: 0.8028 (m-80) REVERT: A 122 TYR cc_start: 0.6784 (OUTLIER) cc_final: 0.6444 (t80) REVERT: A 433 LEU cc_start: 0.9098 (mm) cc_final: 0.8838 (mm) REVERT: A 454 PHE cc_start: 0.8542 (m-10) cc_final: 0.8299 (m-80) outliers start: 44 outliers final: 31 residues processed: 153 average time/residue: 0.1568 time to fit residues: 33.7565 Evaluate side-chains 146 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 114 time to evaluate : 0.803 ------------------------------------------------------------------------------- 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 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 330 ASP 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 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 287 THR Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 383 ASP 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: 0.9980 chunk 47 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 61 optimal weight: 0.0030 chunk 34 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 chunk 57 optimal weight: 8.9990 chunk 0 optimal weight: 0.9990 chunk 42 optimal weight: 8.9990 chunk 74 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 overall best weight: 0.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.4608 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= 0.186 Angle : 0.736 13.559 9052 Z= 0.338 Chirality : 0.041 0.298 1118 Planarity : 0.004 0.040 1094 Dihedral : 4.138 25.661 910 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 6.59 % Allowed : 20.20 % Favored : 73.21 % 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: 1.30 (0.30), residues: 860 helix: 1.68 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -2.43 (0.49), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 377 HIS 0.001 0.001 HIS A 169 PHE 0.012 0.001 PHE B 340 TYR 0.015 0.001 TYR B 260 ARG 0.004 0.000 ARG A 375 *********************** 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 167 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 121 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 214 GLU cc_start: 0.8264 (tt0) cc_final: 0.7480 (tp30) REVERT: B 271 MET cc_start: 0.8383 (ppp) cc_final: 0.8053 (ppp) REVERT: B 364 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8999 (mm) REVERT: B 377 TRP cc_start: 0.6579 (t-100) cc_final: 0.6259 (t-100) REVERT: B 454 PHE cc_start: 0.8439 (m-10) cc_final: 0.8024 (m-80) REVERT: A 122 TYR cc_start: 0.6767 (OUTLIER) cc_final: 0.6433 (t80) REVERT: A 235 MET cc_start: 0.7209 (mtt) cc_final: 0.6732 (mtt) REVERT: A 332 ASP cc_start: 0.8091 (t0) cc_final: 0.7816 (t0) REVERT: A 433 LEU cc_start: 0.9082 (mm) cc_final: 0.8859 (mm) REVERT: A 454 PHE cc_start: 0.8503 (m-10) cc_final: 0.8260 (m-80) outliers start: 46 outliers final: 29 residues processed: 151 average time/residue: 0.1555 time to fit residues: 33.5652 Evaluate side-chains 141 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 110 time to evaluate : 0.814 ------------------------------------------------------------------------------- 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 262 VAL Chi-restraints excluded: chain B residue 266 ILE 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 330 ASP Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 96 LEU 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 269 LEU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 383 ASP 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 27 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 chunk 48 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 83 optimal weight: 4.9990 chunk 69 optimal weight: 0.6980 chunk 38 optimal weight: 7.9990 chunk 6 optimal weight: 0.0980 chunk 43 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7354 moved from start: 0.4740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6646 Z= 0.173 Angle : 0.745 14.185 9052 Z= 0.340 Chirality : 0.040 0.262 1118 Planarity : 0.004 0.039 1094 Dihedral : 4.137 25.756 910 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 5.44 % Allowed : 22.06 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.30), residues: 860 helix: 1.61 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -2.41 (0.50), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 97 HIS 0.001 0.000 HIS A 169 PHE 0.012 0.001 PHE B 358 TYR 0.021 0.001 TYR B 485 ARG 0.003 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 159 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 121 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 214 GLU cc_start: 0.8264 (tt0) cc_final: 0.7483 (tp30) REVERT: B 364 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8995 (mm) REVERT: B 377 TRP cc_start: 0.6509 (t-100) cc_final: 0.6183 (t-100) REVERT: B 454 PHE cc_start: 0.8402 (m-10) cc_final: 0.7993 (m-80) REVERT: A 122 TYR cc_start: 0.6774 (OUTLIER) cc_final: 0.6434 (t80) REVERT: A 291 MET cc_start: 0.7472 (ppp) cc_final: 0.7266 (ppp) REVERT: A 433 LEU cc_start: 0.9079 (mm) cc_final: 0.8839 (mm) REVERT: A 454 PHE cc_start: 0.8483 (m-10) cc_final: 0.8147 (m-80) outliers start: 38 outliers final: 29 residues processed: 144 average time/residue: 0.1363 time to fit residues: 28.6374 Evaluate side-chains 142 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 111 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 266 ILE 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 358 PHE 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 B residue 481 GLN 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 330 ASP Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 383 ASP 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 9 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 60 optimal weight: 0.5980 chunk 70 optimal weight: 8.9990 chunk 46 optimal weight: 0.0870 chunk 82 optimal weight: 6.9990 chunk 51 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 33 optimal weight: 0.0970 chunk 49 optimal weight: 8.9990 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7339 moved from start: 0.4882 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= 0.171 Angle : 0.749 14.661 9052 Z= 0.342 Chirality : 0.042 0.395 1118 Planarity : 0.004 0.040 1094 Dihedral : 4.150 25.704 910 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 4.87 % Allowed : 24.21 % 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: 1.17 (0.30), residues: 860 helix: 1.60 (0.20), residues: 678 sheet: None (None), residues: 0 loop : -2.45 (0.49), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 97 HIS 0.001 0.000 HIS A 169 PHE 0.020 0.001 PHE A 322 TYR 0.021 0.001 TYR B 485 ARG 0.002 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 151 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 117 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 214 GLU cc_start: 0.8261 (tt0) cc_final: 0.7646 (mm-30) REVERT: B 364 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8993 (mm) REVERT: B 377 TRP cc_start: 0.6536 (t-100) cc_final: 0.6203 (t-100) REVERT: B 454 PHE cc_start: 0.8370 (m-10) cc_final: 0.7928 (m-80) REVERT: A 122 TYR cc_start: 0.6740 (OUTLIER) cc_final: 0.6397 (t80) REVERT: A 291 MET cc_start: 0.7318 (ppp) cc_final: 0.7000 (ppp) REVERT: A 433 LEU cc_start: 0.9086 (mm) cc_final: 0.8844 (mm) REVERT: A 454 PHE cc_start: 0.8416 (m-10) cc_final: 0.8085 (m-80) outliers start: 34 outliers final: 28 residues processed: 137 average time/residue: 0.1315 time to fit residues: 26.0445 Evaluate side-chains 144 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 114 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 266 ILE 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 358 PHE 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 B residue 481 GLN Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 122 TYR Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 461 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 24 optimal weight: 0.8980 chunk 16 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 40 optimal weight: 9.9990 chunk 7 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 75 optimal weight: 0.0570 chunk 79 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 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 0.036 6646 Z= 0.172 Angle : 0.745 14.721 9052 Z= 0.342 Chirality : 0.041 0.183 1118 Planarity : 0.004 0.040 1094 Dihedral : 4.136 25.771 910 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 6.16 % Allowed : 23.50 % Favored : 70.34 % 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: 1.60 (0.20), residues: 678 sheet: None (None), residues: 0 loop : -2.47 (0.49), residues: 182 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 0.019 0.001 PHE A 322 TYR 0.023 0.001 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 159 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 116 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 MET cc_start: 0.8250 (mtm) cc_final: 0.8006 (mpp) REVERT: B 214 GLU cc_start: 0.8303 (tt0) cc_final: 0.7689 (mm-30) REVERT: B 364 LEU cc_start: 0.9238 (tp) cc_final: 0.9001 (mm) REVERT: B 377 TRP cc_start: 0.6545 (t-100) cc_final: 0.6196 (t-100) REVERT: B 454 PHE cc_start: 0.8378 (m-10) cc_final: 0.7931 (m-80) REVERT: A 122 TYR cc_start: 0.6780 (OUTLIER) cc_final: 0.6446 (t80) REVERT: A 181 SER cc_start: 0.7392 (OUTLIER) cc_final: 0.7170 (t) REVERT: A 291 MET cc_start: 0.7111 (ppp) cc_final: 0.6786 (ppp) REVERT: A 433 LEU cc_start: 0.9071 (mm) cc_final: 0.8813 (mm) REVERT: A 454 PHE cc_start: 0.8413 (m-10) cc_final: 0.8083 (m-80) outliers start: 43 outliers final: 28 residues processed: 144 average time/residue: 0.1305 time to fit residues: 27.3993 Evaluate side-chains 140 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 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 102 SER Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 358 PHE 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 B residue 481 GLN 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 145 LEU Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 383 ASP 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 79 optimal weight: 4.9990 chunk 46 optimal weight: 0.0060 chunk 33 optimal weight: 0.0040 chunk 60 optimal weight: 0.2980 chunk 23 optimal weight: 10.0000 chunk 69 optimal weight: 0.6980 chunk 73 optimal weight: 0.6980 chunk 76 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 49 optimal weight: 30.0000 overall best weight: 0.3408 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 HIS ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.5090 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= 0.166 Angle : 0.766 15.265 9052 Z= 0.351 Chirality : 0.040 0.241 1118 Planarity : 0.004 0.040 1094 Dihedral : 4.137 25.788 910 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 4.15 % Allowed : 26.07 % Favored : 69.77 % 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: 1.11 (0.30), residues: 860 helix: 1.54 (0.20), residues: 678 sheet: None (None), residues: 0 loop : -2.43 (0.48), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 97 HIS 0.002 0.000 HIS B 477 PHE 0.018 0.001 PHE A 322 TYR 0.023 0.001 TYR B 485 ARG 0.002 0.000 ARG A 375 *********************** 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 fitting. rotamer outliers: 29 poor density : 116 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 MET cc_start: 0.8209 (mtm) cc_final: 0.7984 (mpp) REVERT: B 145 LEU cc_start: 0.8429 (mp) cc_final: 0.8226 (mp) REVERT: B 214 GLU cc_start: 0.8299 (tt0) cc_final: 0.7690 (mm-30) REVERT: B 364 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8999 (mm) REVERT: B 377 TRP cc_start: 0.6522 (t-100) cc_final: 0.6215 (t-100) REVERT: B 454 PHE cc_start: 0.8352 (m-10) cc_final: 0.8142 (m-80) REVERT: A 122 TYR cc_start: 0.6849 (OUTLIER) cc_final: 0.6486 (t80) REVERT: A 181 SER cc_start: 0.7361 (OUTLIER) cc_final: 0.7137 (t) REVERT: A 235 MET cc_start: 0.7123 (mtt) cc_final: 0.6671 (mtt) REVERT: A 291 MET cc_start: 0.7266 (ppp) cc_final: 0.6945 (ppp) REVERT: A 306 VAL cc_start: 0.9048 (t) cc_final: 0.8840 (p) REVERT: A 424 LEU cc_start: 0.8254 (tp) cc_final: 0.8029 (mt) REVERT: A 433 LEU cc_start: 0.9070 (mm) cc_final: 0.8815 (mm) REVERT: A 454 PHE cc_start: 0.8364 (m-10) cc_final: 0.8047 (m-80) REVERT: A 490 LEU cc_start: 0.8856 (mt) cc_final: 0.7878 (mt) outliers start: 29 outliers final: 24 residues processed: 134 average time/residue: 0.1325 time to fit residues: 25.6843 Evaluate side-chains 136 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 109 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 358 PHE 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 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 240 LEU 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 330 ASP Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 383 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 38 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 85 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 68 optimal weight: 0.0470 chunk 7 optimal weight: 0.9990 chunk 52 optimal weight: 0.0060 chunk 41 optimal weight: 0.3980 chunk 54 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 overall best weight: 0.3494 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.5154 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= 0.176 Angle : 0.789 15.536 9052 Z= 0.363 Chirality : 0.040 0.187 1118 Planarity : 0.004 0.040 1094 Dihedral : 4.150 25.650 910 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 4.30 % Allowed : 26.36 % Favored : 69.34 % 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: 1.04 (0.30), residues: 860 helix: 1.51 (0.20), residues: 678 sheet: None (None), residues: 0 loop : -2.50 (0.48), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 97 HIS 0.001 0.000 HIS A 477 PHE 0.020 0.001 PHE A 322 TYR 0.026 0.001 TYR B 485 ARG 0.004 0.000 ARG A 475 ********************** 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 143 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 113 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 214 GLU cc_start: 0.8288 (tt0) cc_final: 0.7674 (mm-30) REVERT: B 254 LEU cc_start: 0.8984 (mp) cc_final: 0.8774 (tt) REVERT: B 364 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8993 (mm) REVERT: B 377 TRP cc_start: 0.6512 (t-100) cc_final: 0.6193 (t-100) REVERT: B 454 PHE cc_start: 0.8361 (m-10) cc_final: 0.7999 (m-80) REVERT: A 122 TYR cc_start: 0.6825 (OUTLIER) cc_final: 0.6467 (t80) REVERT: A 181 SER cc_start: 0.7366 (OUTLIER) cc_final: 0.7133 (t) REVERT: A 235 MET cc_start: 0.7011 (mtt) cc_final: 0.6593 (mtt) REVERT: A 291 MET cc_start: 0.7109 (ppp) cc_final: 0.6870 (ppp) REVERT: A 424 LEU cc_start: 0.8137 (tp) cc_final: 0.7912 (mt) REVERT: A 433 LEU cc_start: 0.9052 (mm) cc_final: 0.8773 (mm) REVERT: A 454 PHE cc_start: 0.8362 (m-10) cc_final: 0.8055 (m-80) outliers start: 30 outliers final: 24 residues processed: 134 average time/residue: 0.1324 time to fit residues: 25.9451 Evaluate side-chains 137 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 110 time to evaluate : 0.749 ------------------------------------------------------------------------------- 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 182 VAL Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 358 PHE 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 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 240 LEU 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 330 ASP Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 383 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 62 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 18 optimal weight: 0.0370 chunk 68 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 12 optimal weight: 5.9990 chunk 59 optimal weight: 0.0770 chunk 3 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 overall best weight: 0.7420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.097931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.083854 restraints weight = 31036.225| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 4.37 r_work (final): 0.3911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.5249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6646 Z= 0.182 Angle : 0.790 15.038 9052 Z= 0.369 Chirality : 0.040 0.181 1118 Planarity : 0.004 0.040 1094 Dihedral : 4.098 25.811 908 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 4.44 % Allowed : 26.36 % Favored : 69.20 % 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: 0.93 (0.30), residues: 860 helix: 1.42 (0.20), residues: 672 sheet: None (None), residues: 0 loop : -2.36 (0.48), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 97 HIS 0.001 0.000 HIS A 169 PHE 0.018 0.001 PHE A 322 TYR 0.022 0.001 TYR B 485 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: 1676.37 seconds wall clock time: 31 minutes 44.62 seconds (1904.62 seconds total)