Starting phenix.real_space_refine on Tue Jan 14 06:30:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xit_38389/01_2025/8xit_38389.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xit_38389/01_2025/8xit_38389.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xit_38389/01_2025/8xit_38389.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xit_38389/01_2025/8xit_38389.map" model { file = "/net/cci-nas-00/data/ceres_data/8xit_38389/01_2025/8xit_38389.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xit_38389/01_2025/8xit_38389.cif" } resolution = 3.2 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= 0.002 sd= 0.025 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 60 5.16 5 C 3968 2.51 5 N 950 2.21 5 O 1024 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 6002 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3001 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 16, 'TRANS': 375} Chain breaks: 6 Chain: "B" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3001 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 16, 'TRANS': 375} Chain breaks: 6 Time building chain proxies: 4.02, per 1000 atoms: 0.67 Number of scatterers: 6002 At special positions: 0 Unit cell: (90.1, 92.65, 95.2, 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 60 16.00 O 1024 8.00 N 950 7.00 C 3968 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: 1.51 Conformation dependent library (CDL) restraints added in 894.5 milliseconds 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1428 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 0 sheets defined 92.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 16 through 39 Processing helix chain 'A' and resid 40 through 42 No H-bonds generated for 'chain 'A' and resid 40 through 42' Processing helix chain 'A' and resid 43 through 49 Processing helix chain 'A' and resid 134 through 159 removed outlier: 5.087A pdb=" N LYS A 141 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ALA A 142 " --> pdb=" O PHE A 138 " (cutoff:3.500A) Proline residue: A 150 - end of helix Processing helix chain 'A' and resid 161 through 182 removed outlier: 3.834A pdb=" N MET A 165 " --> pdb=" O TYR A 161 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE A 166 " --> pdb=" O PRO A 162 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR A 167 " --> pdb=" O ILE A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 214 removed outlier: 3.586A pdb=" N TYR A 214 " --> pdb=" O LEU A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 249 removed outlier: 4.271A pdb=" N VAL A 235 " --> pdb=" O LEU A 231 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU A 236 " --> pdb=" O ALA A 232 " (cutoff:3.500A) Proline residue: A 239 - end of helix Processing helix chain 'A' and resid 252 through 272 Processing helix chain 'A' and resid 297 through 314 removed outlier: 3.594A pdb=" N ALA A 312 " --> pdb=" O ASN A 308 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A 314 " --> pdb=" O GLY A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 328 removed outlier: 3.516A pdb=" N THR A 325 " --> pdb=" O TRP A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 338 Processing helix chain 'A' and resid 338 through 348 removed outlier: 4.183A pdb=" N ILE A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 371 removed outlier: 3.622A pdb=" N ASN A 365 " --> pdb=" O ASP A 361 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TRP A 366 " --> pdb=" O LEU A 362 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LEU A 369 " --> pdb=" O ASN A 365 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP A 371 " --> pdb=" O GLU A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 394 removed outlier: 3.987A pdb=" N ALA A 394 " --> pdb=" O THR A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 433 removed outlier: 3.573A pdb=" N ASP A 433 " --> pdb=" O GLY A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 491 Processing helix chain 'A' and resid 492 through 494 No H-bonds generated for 'chain 'A' and resid 492 through 494' Processing helix chain 'A' and resid 497 through 499 No H-bonds generated for 'chain 'A' and resid 497 through 499' Processing helix chain 'A' and resid 500 through 519 removed outlier: 3.636A pdb=" N ASN A 504 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N PHE A 509 " --> pdb=" O PHE A 505 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP A 515 " --> pdb=" O ILE A 511 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER A 517 " --> pdb=" O MET A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 547 Processing helix chain 'A' and resid 567 through 584 removed outlier: 3.602A pdb=" N ILE A 571 " --> pdb=" O TRP A 567 " (cutoff:3.500A) Proline residue: A 581 - end of helix Processing helix chain 'B' and resid 17 through 39 Processing helix chain 'B' and resid 40 through 42 No H-bonds generated for 'chain 'B' and resid 40 through 42' Processing helix chain 'B' and resid 43 through 49 Processing helix chain 'B' and resid 134 through 159 removed outlier: 5.067A pdb=" N LYS B 141 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ALA B 142 " --> pdb=" O PHE B 138 " (cutoff:3.500A) Proline residue: B 150 - end of helix Processing helix chain 'B' and resid 161 through 182 removed outlier: 3.868A pdb=" N MET B 165 " --> pdb=" O TYR B 161 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N PHE B 166 " --> pdb=" O PRO B 162 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR B 167 " --> pdb=" O ILE B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 214 removed outlier: 3.602A pdb=" N TYR B 214 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 249 removed outlier: 4.313A pdb=" N VAL B 235 " --> pdb=" O LEU B 231 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LEU B 236 " --> pdb=" O ALA B 232 " (cutoff:3.500A) Proline residue: B 239 - end of helix Processing helix chain 'B' and resid 252 through 272 Processing helix chain 'B' and resid 297 through 314 removed outlier: 3.650A pdb=" N ALA B 312 " --> pdb=" O ASN B 308 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU B 314 " --> pdb=" O GLY B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 329 removed outlier: 3.833A pdb=" N MET B 323 " --> pdb=" O PRO B 319 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N GLU B 324 " --> pdb=" O ILE B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 338 Processing helix chain 'B' and resid 338 through 348 removed outlier: 4.167A pdb=" N ILE B 342 " --> pdb=" O LEU B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 371 removed outlier: 4.456A pdb=" N THR B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N LEU B 369 " --> pdb=" O ASN B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 394 Processing helix chain 'B' and resid 424 through 433 removed outlier: 3.630A pdb=" N ASP B 433 " --> pdb=" O GLY B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 491 removed outlier: 3.939A pdb=" N ARG B 467 " --> pdb=" O LYS B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 499 No H-bonds generated for 'chain 'B' and resid 497 through 499' Processing helix chain 'B' and resid 500 through 519 removed outlier: 3.735A pdb=" N ASN B 504 " --> pdb=" O LEU B 500 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE B 509 " --> pdb=" O PHE B 505 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASP B 515 " --> pdb=" O ILE B 511 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER B 517 " --> pdb=" O MET B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 547 removed outlier: 3.509A pdb=" N MET B 547 " --> pdb=" O VAL B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 584 removed outlier: 3.646A pdb=" N ILE B 571 " --> pdb=" O TRP B 567 " (cutoff:3.500A) Proline residue: B 581 - end of helix 502 hydrogen bonds defined for protein. 1506 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: 1.74 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: 1824 1.34 - 1.46: 1310 1.46 - 1.58: 2886 1.58 - 1.69: 0 1.69 - 1.81: 104 Bond restraints: 6124 Sorted by residual: bond pdb=" CA LEU B 338 " pdb=" C LEU B 338 " ideal model delta sigma weight residual 1.524 1.536 -0.012 1.26e-02 6.30e+03 9.08e-01 bond pdb=" CA THR B 348 " pdb=" C THR B 348 " ideal model delta sigma weight residual 1.522 1.535 -0.013 1.38e-02 5.25e+03 8.63e-01 bond pdb=" CA LEU A 338 " pdb=" C LEU A 338 " ideal model delta sigma weight residual 1.522 1.533 -0.011 1.26e-02 6.30e+03 7.92e-01 bond pdb=" CA ASN A 149 " pdb=" C ASN A 149 " ideal model delta sigma weight residual 1.520 1.531 -0.011 1.23e-02 6.61e+03 7.92e-01 bond pdb=" CA ASN B 149 " pdb=" C ASN B 149 " ideal model delta sigma weight residual 1.520 1.531 -0.010 1.23e-02 6.61e+03 6.88e-01 ... (remaining 6119 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 8057 1.64 - 3.28: 181 3.28 - 4.92: 46 4.92 - 6.57: 9 6.57 - 8.21: 3 Bond angle restraints: 8296 Sorted by residual: angle pdb=" N LEU B 338 " pdb=" CA LEU B 338 " pdb=" C LEU B 338 " ideal model delta sigma weight residual 109.81 118.02 -8.21 2.21e+00 2.05e-01 1.38e+01 angle pdb=" CA PRO B 316 " pdb=" C PRO B 316 " pdb=" N ALA B 317 " ideal model delta sigma weight residual 114.58 117.79 -3.21 1.16e+00 7.43e-01 7.67e+00 angle pdb=" N TYR B 161 " pdb=" CA TYR B 161 " pdb=" C TYR B 161 " ideal model delta sigma weight residual 109.81 115.59 -5.78 2.21e+00 2.05e-01 6.84e+00 angle pdb=" N PRO B 239 " pdb=" CA PRO B 239 " pdb=" C PRO B 239 " ideal model delta sigma weight residual 110.70 113.77 -3.07 1.22e+00 6.72e-01 6.33e+00 angle pdb=" CA MET B 326 " pdb=" CB MET B 326 " pdb=" CG MET B 326 " ideal model delta sigma weight residual 114.10 119.02 -4.92 2.00e+00 2.50e-01 6.06e+00 ... (remaining 8291 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.09: 3254 17.09 - 34.17: 267 34.17 - 51.25: 54 51.25 - 68.34: 10 68.34 - 85.42: 5 Dihedral angle restraints: 3590 sinusoidal: 1364 harmonic: 2226 Sorted by residual: dihedral pdb=" CG ARG B 192 " pdb=" CD ARG B 192 " pdb=" NE ARG B 192 " pdb=" CZ ARG B 192 " ideal model delta sinusoidal sigma weight residual 180.00 135.70 44.30 2 1.50e+01 4.44e-03 1.04e+01 dihedral pdb=" CG ARG A 192 " pdb=" CD ARG A 192 " pdb=" NE ARG A 192 " pdb=" CZ ARG A 192 " ideal model delta sinusoidal sigma weight residual 180.00 135.77 44.23 2 1.50e+01 4.44e-03 1.04e+01 dihedral pdb=" CB GLU B 466 " pdb=" CG GLU B 466 " pdb=" CD GLU B 466 " pdb=" OE1 GLU B 466 " ideal model delta sinusoidal sigma weight residual 0.00 -85.42 85.42 1 3.00e+01 1.11e-03 9.82e+00 ... (remaining 3587 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 732 0.040 - 0.081: 203 0.081 - 0.121: 47 0.121 - 0.161: 6 0.161 - 0.201: 2 Chirality restraints: 990 Sorted by residual: chirality pdb=" CA LEU B 338 " pdb=" N LEU B 338 " pdb=" C LEU B 338 " pdb=" CB LEU B 338 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA LEU A 338 " pdb=" N LEU A 338 " pdb=" C LEU A 338 " pdb=" CB LEU A 338 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.42e-01 chirality pdb=" CA ILE A 491 " pdb=" N ILE A 491 " pdb=" C ILE A 491 " pdb=" CB ILE A 491 " both_signs ideal model delta sigma weight residual False 2.43 2.28 0.15 2.00e-01 2.50e+01 5.51e-01 ... (remaining 987 not shown) Planarity restraints: 1012 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 534 " 0.020 2.00e-02 2.50e+03 1.77e-02 6.23e+00 pdb=" CG TYR A 534 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TYR A 534 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR A 534 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 534 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 534 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR A 534 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 534 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 534 " -0.020 2.00e-02 2.50e+03 1.76e-02 6.22e+00 pdb=" CG TYR B 534 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TYR B 534 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR B 534 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR B 534 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 534 " -0.010 2.00e-02 2.50e+03 pdb=" CZ TYR B 534 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 534 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 580 " 0.034 5.00e-02 4.00e+02 5.18e-02 4.30e+00 pdb=" N PRO B 581 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO B 581 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 581 " 0.029 5.00e-02 4.00e+02 ... (remaining 1009 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1471 2.81 - 3.33: 6264 3.33 - 3.85: 9558 3.85 - 4.38: 9689 4.38 - 4.90: 18147 Nonbonded interactions: 45129 Sorted by model distance: nonbonded pdb=" ND2 ASN B 34 " pdb=" O LEU B 231 " model vdw 2.287 3.120 nonbonded pdb=" OG SER B 175 " pdb=" O ALA B 191 " model vdw 2.303 3.040 nonbonded pdb=" ND2 ASN A 34 " pdb=" O LEU A 231 " model vdw 2.338 3.120 nonbonded pdb=" OG SER A 175 " pdb=" O ALA A 191 " model vdw 2.341 3.040 nonbonded pdb=" O ASP B 387 " pdb=" OG1 THR B 390 " model vdw 2.471 3.040 ... (remaining 45124 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 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: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.210 Find NCS groups from input model: 0.180 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 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 : 0.003 0.032 6124 Z= 0.213 Angle : 0.644 8.208 8296 Z= 0.333 Chirality : 0.040 0.201 990 Planarity : 0.005 0.052 1012 Dihedral : 13.312 85.423 2162 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % 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: 3.41 (0.32), residues: 756 helix: 2.84 (0.20), residues: 668 sheet: None (None), residues: 0 loop : -2.88 (0.62), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 321 HIS 0.001 0.000 HIS B 530 PHE 0.018 0.001 PHE B 241 TYR 0.043 0.002 TYR A 534 ARG 0.003 0.000 ARG B 469 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.649 Fit side-chains REVERT: B 233 MET cc_start: 0.8575 (ppp) cc_final: 0.8301 (tmm) REVERT: B 323 MET cc_start: 0.6273 (tpt) cc_final: 0.5950 (tpt) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.1863 time to fit residues: 25.0971 Evaluate side-chains 94 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 32 optimal weight: 0.9980 chunk 20 optimal weight: 8.9990 chunk 39 optimal weight: 5.9990 chunk 31 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 GLN B 34 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.169603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.119606 restraints weight = 7508.631| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.64 r_work: 0.3229 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.0936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6124 Z= 0.252 Angle : 0.647 12.323 8296 Z= 0.325 Chirality : 0.040 0.164 990 Planarity : 0.005 0.048 1012 Dihedral : 3.686 14.815 826 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.47 % Allowed : 9.66 % Favored : 89.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.81 (0.32), residues: 756 helix: 3.10 (0.20), residues: 672 sheet: None (None), residues: 0 loop : -3.01 (0.61), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 321 HIS 0.002 0.001 HIS B 329 PHE 0.016 0.001 PHE B 241 TYR 0.026 0.002 TYR A 534 ARG 0.002 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 95 time to evaluate : 0.584 Fit side-chains REVERT: A 462 GLN cc_start: 0.8062 (mp10) cc_final: 0.7794 (mp10) REVERT: B 233 MET cc_start: 0.9053 (ppp) cc_final: 0.8737 (tmm) outliers start: 3 outliers final: 2 residues processed: 97 average time/residue: 0.1736 time to fit residues: 22.3850 Evaluate side-chains 94 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 92 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 362 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 34 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 69 optimal weight: 0.4980 chunk 52 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 36 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 56 optimal weight: 5.9990 chunk 17 optimal weight: 0.0970 chunk 9 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.173503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.125240 restraints weight = 7498.995| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.40 r_work: 0.3305 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6124 Z= 0.177 Angle : 0.604 13.659 8296 Z= 0.297 Chirality : 0.037 0.140 990 Planarity : 0.004 0.040 1012 Dihedral : 3.552 14.005 826 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.93 % Allowed : 11.99 % Favored : 87.07 % 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: 4.01 (0.32), residues: 756 helix: 3.30 (0.20), residues: 668 sheet: None (None), residues: 0 loop : -3.29 (0.56), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 321 HIS 0.001 0.001 HIS B 17 PHE 0.016 0.001 PHE B 241 TYR 0.019 0.001 TYR A 534 ARG 0.002 0.000 ARG B 469 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 101 time to evaluate : 0.595 Fit side-chains REVERT: A 326 MET cc_start: 0.8267 (ppp) cc_final: 0.7873 (ppp) REVERT: A 432 ASP cc_start: 0.6784 (m-30) cc_final: 0.6576 (m-30) REVERT: B 233 MET cc_start: 0.8970 (ppp) cc_final: 0.8646 (tmm) outliers start: 6 outliers final: 4 residues processed: 105 average time/residue: 0.1629 time to fit residues: 23.0964 Evaluate side-chains 99 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 95 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 577 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.172369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.121724 restraints weight = 7535.711| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.73 r_work: 0.3219 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6124 Z= 0.193 Angle : 0.602 14.033 8296 Z= 0.294 Chirality : 0.037 0.136 990 Planarity : 0.004 0.039 1012 Dihedral : 3.456 15.382 826 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.87 % Allowed : 12.62 % Favored : 85.51 % 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: 4.07 (0.32), residues: 756 helix: 3.35 (0.20), residues: 668 sheet: None (None), residues: 0 loop : -3.35 (0.55), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 321 HIS 0.001 0.000 HIS A 530 PHE 0.015 0.001 PHE B 241 TYR 0.014 0.001 TYR A 534 ARG 0.004 0.000 ARG B 393 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.606 Fit side-chains REVERT: A 326 MET cc_start: 0.8369 (ppp) cc_final: 0.7994 (ppp) REVERT: A 432 ASP cc_start: 0.6898 (m-30) cc_final: 0.6666 (m-30) REVERT: A 462 GLN cc_start: 0.7957 (mp10) cc_final: 0.7704 (mp10) REVERT: B 233 MET cc_start: 0.9036 (ppp) cc_final: 0.8802 (tmm) outliers start: 12 outliers final: 7 residues processed: 106 average time/residue: 0.1525 time to fit residues: 22.0750 Evaluate side-chains 104 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 577 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 73 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 27 optimal weight: 20.0000 chunk 25 optimal weight: 4.9990 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 358 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.166574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.117284 restraints weight = 7483.503| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.48 r_work: 0.3149 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 6124 Z= 0.344 Angle : 0.678 14.355 8296 Z= 0.334 Chirality : 0.040 0.147 990 Planarity : 0.005 0.041 1012 Dihedral : 3.536 15.802 826 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.34 % Allowed : 14.17 % Favored : 83.49 % 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: 3.82 (0.32), residues: 756 helix: 3.14 (0.20), residues: 672 sheet: None (None), residues: 0 loop : -3.42 (0.57), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 366 HIS 0.001 0.000 HIS A 530 PHE 0.016 0.001 PHE A 166 TYR 0.015 0.002 TYR B 538 ARG 0.006 0.000 ARG B 393 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.655 Fit side-chains REVERT: A 326 MET cc_start: 0.8386 (ppp) cc_final: 0.8070 (ppp) REVERT: A 432 ASP cc_start: 0.6864 (m-30) cc_final: 0.6622 (m-30) REVERT: A 462 GLN cc_start: 0.7994 (mp10) cc_final: 0.7720 (mp10) REVERT: B 195 GLN cc_start: 0.8867 (OUTLIER) cc_final: 0.8601 (mt0) REVERT: B 233 MET cc_start: 0.9042 (ppp) cc_final: 0.8780 (tmm) outliers start: 15 outliers final: 10 residues processed: 112 average time/residue: 0.1617 time to fit residues: 24.7676 Evaluate side-chains 111 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 476 CYS Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 577 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 21 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 67 optimal weight: 7.9990 chunk 10 optimal weight: 0.6980 chunk 39 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.169060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.118766 restraints weight = 7382.623| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.64 r_work: 0.3204 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6124 Z= 0.230 Angle : 0.634 14.749 8296 Z= 0.309 Chirality : 0.038 0.143 990 Planarity : 0.004 0.039 1012 Dihedral : 3.528 15.241 826 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.49 % Allowed : 14.80 % Favored : 82.71 % 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: 3.89 (0.32), residues: 756 helix: 3.21 (0.20), residues: 672 sheet: None (None), residues: 0 loop : -3.52 (0.56), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 366 HIS 0.001 0.000 HIS A 530 PHE 0.015 0.001 PHE B 241 TYR 0.012 0.001 TYR B 538 ARG 0.001 0.000 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 0.635 Fit side-chains REVERT: A 326 MET cc_start: 0.8342 (ppp) cc_final: 0.8017 (ppp) REVERT: A 432 ASP cc_start: 0.6878 (m-30) cc_final: 0.6641 (m-30) REVERT: A 519 MET cc_start: 0.7833 (mmm) cc_final: 0.7464 (mmp) REVERT: B 233 MET cc_start: 0.8999 (ppp) cc_final: 0.8752 (tmm) REVERT: B 519 MET cc_start: 0.7816 (mmm) cc_final: 0.7441 (mmp) outliers start: 16 outliers final: 7 residues processed: 112 average time/residue: 0.1643 time to fit residues: 24.8985 Evaluate side-chains 105 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 98 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 476 CYS Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 577 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 42 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 6 optimal weight: 0.0030 overall best weight: 0.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 GLN B 195 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.170258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.120552 restraints weight = 7407.731| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.51 r_work: 0.3222 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6124 Z= 0.214 Angle : 0.636 15.109 8296 Z= 0.308 Chirality : 0.038 0.138 990 Planarity : 0.004 0.038 1012 Dihedral : 3.544 16.801 826 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.71 % Allowed : 16.20 % Favored : 82.09 % 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: 3.97 (0.32), residues: 756 helix: 3.25 (0.20), residues: 672 sheet: None (None), residues: 0 loop : -3.47 (0.55), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 321 HIS 0.001 0.000 HIS A 530 PHE 0.014 0.001 PHE B 241 TYR 0.011 0.001 TYR B 538 ARG 0.002 0.000 ARG B 393 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.617 Fit side-chains REVERT: A 326 MET cc_start: 0.8321 (ppp) cc_final: 0.7992 (ppp) REVERT: A 432 ASP cc_start: 0.6900 (m-30) cc_final: 0.6644 (m-30) REVERT: B 233 MET cc_start: 0.8959 (ppp) cc_final: 0.8716 (tmm) outliers start: 11 outliers final: 10 residues processed: 112 average time/residue: 0.1564 time to fit residues: 23.8888 Evaluate side-chains 109 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 476 CYS Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 362 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 48 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 58 optimal weight: 0.0370 chunk 52 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 37 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 41 optimal weight: 0.1980 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.173050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.122492 restraints weight = 7516.274| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.65 r_work: 0.3267 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6124 Z= 0.174 Angle : 0.614 14.553 8296 Z= 0.294 Chirality : 0.037 0.132 990 Planarity : 0.004 0.039 1012 Dihedral : 3.495 16.931 826 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.02 % Allowed : 16.36 % Favored : 81.62 % 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: 4.17 (0.32), residues: 756 helix: 3.39 (0.20), residues: 672 sheet: None (None), residues: 0 loop : -3.36 (0.56), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 321 HIS 0.001 0.000 HIS B 17 PHE 0.014 0.001 PHE B 241 TYR 0.009 0.001 TYR B 344 ARG 0.001 0.000 ARG B 393 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.682 Fit side-chains REVERT: A 326 MET cc_start: 0.8378 (ppp) cc_final: 0.8083 (ppp) REVERT: A 432 ASP cc_start: 0.6973 (m-30) cc_final: 0.6701 (m-30) REVERT: B 233 MET cc_start: 0.8901 (ppp) cc_final: 0.8672 (tmm) outliers start: 13 outliers final: 9 residues processed: 115 average time/residue: 0.1588 time to fit residues: 24.9354 Evaluate side-chains 110 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 577 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 76 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 20 optimal weight: 0.0270 chunk 27 optimal weight: 10.0000 chunk 53 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 overall best weight: 0.6640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.172437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.122372 restraints weight = 7568.971| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.54 r_work: 0.3270 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6124 Z= 0.188 Angle : 0.633 15.864 8296 Z= 0.301 Chirality : 0.037 0.133 990 Planarity : 0.004 0.037 1012 Dihedral : 3.443 16.130 826 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.71 % Allowed : 16.82 % Favored : 81.46 % 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: 4.12 (0.32), residues: 756 helix: 3.35 (0.20), residues: 672 sheet: None (None), residues: 0 loop : -3.35 (0.55), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 321 HIS 0.000 0.000 HIS B 329 PHE 0.014 0.001 PHE B 241 TYR 0.010 0.001 TYR B 344 ARG 0.002 0.000 ARG B 393 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.577 Fit side-chains REVERT: A 326 MET cc_start: 0.8374 (ppp) cc_final: 0.8067 (ppp) REVERT: A 432 ASP cc_start: 0.7046 (m-30) cc_final: 0.6778 (m-30) REVERT: B 233 MET cc_start: 0.8882 (ppp) cc_final: 0.8668 (tmm) outliers start: 11 outliers final: 11 residues processed: 113 average time/residue: 0.1498 time to fit residues: 23.1488 Evaluate side-chains 112 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 577 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 33 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 70 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 63 optimal weight: 9.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.167835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.115992 restraints weight = 7547.115| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.81 r_work: 0.3170 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6124 Z= 0.287 Angle : 0.668 15.137 8296 Z= 0.326 Chirality : 0.040 0.147 990 Planarity : 0.004 0.038 1012 Dihedral : 3.491 16.798 826 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.02 % Allowed : 16.36 % Favored : 81.62 % 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: 3.90 (0.32), residues: 756 helix: 3.20 (0.20), residues: 672 sheet: None (None), residues: 0 loop : -3.35 (0.55), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 366 HIS 0.001 0.000 HIS B 17 PHE 0.014 0.001 PHE A 166 TYR 0.013 0.001 TYR B 538 ARG 0.001 0.000 ARG A 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 0.632 Fit side-chains REVERT: A 326 MET cc_start: 0.8388 (ppp) cc_final: 0.8086 (ppp) REVERT: A 432 ASP cc_start: 0.7124 (m-30) cc_final: 0.6849 (m-30) REVERT: B 233 MET cc_start: 0.8983 (ppp) cc_final: 0.8733 (tmm) outliers start: 13 outliers final: 11 residues processed: 111 average time/residue: 0.1614 time to fit residues: 24.3880 Evaluate side-chains 111 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 577 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 67 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 31 optimal weight: 0.0770 chunk 35 optimal weight: 0.5980 chunk 66 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.171540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.120748 restraints weight = 7665.480| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.74 r_work: 0.3237 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6124 Z= 0.185 Angle : 0.640 16.139 8296 Z= 0.306 Chirality : 0.038 0.138 990 Planarity : 0.004 0.038 1012 Dihedral : 3.501 16.479 826 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.71 % Allowed : 17.45 % Favored : 80.84 % 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: 4.07 (0.32), residues: 756 helix: 3.31 (0.20), residues: 672 sheet: None (None), residues: 0 loop : -3.31 (0.55), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 321 HIS 0.001 0.000 HIS B 17 PHE 0.013 0.001 PHE B 241 TYR 0.010 0.001 TYR B 538 ARG 0.002 0.000 ARG A 393 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2974.20 seconds wall clock time: 54 minutes 25.58 seconds (3265.58 seconds total)