Starting phenix.real_space_refine on Wed Mar 12 14:42:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y5x_38955/03_2025/8y5x_38955.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y5x_38955/03_2025/8y5x_38955.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y5x_38955/03_2025/8y5x_38955.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y5x_38955/03_2025/8y5x_38955.map" model { file = "/net/cci-nas-00/data/ceres_data/8y5x_38955/03_2025/8y5x_38955.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y5x_38955/03_2025/8y5x_38955.cif" } resolution = 3.25 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= 0.001 sd= 0.044 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: 5 Type Number sf(0) Gaussians S 56 5.16 5 Na 2 4.78 5 C 5394 2.51 5 N 1222 2.21 5 O 1358 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8032 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 4010 Classifications: {'peptide': 512} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 30, 'TRANS': 481} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 4010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 4010 Classifications: {'peptide': 512} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 30, 'TRANS': 481} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 6 Unusual residues: {' NA': 1, 'SO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 6 Unusual residues: {' NA': 1, 'SO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.21, per 1000 atoms: 0.65 Number of scatterers: 8032 At special positions: 0 Unit cell: (116.399, 92.9514, 80.3904, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 56 16.00 Na 2 11.00 O 1358 8.00 N 1222 7.00 C 5394 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: 2.02 Conformation dependent library (CDL) restraints added in 1.2 seconds 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1936 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 0 sheets defined 81.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 2 through 10 Processing helix chain 'A' and resid 10 through 23 removed outlier: 3.597A pdb=" N LEU A 23 " --> pdb=" O THR A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 29 Processing helix chain 'A' and resid 32 through 51 removed outlier: 3.547A pdb=" N GLU A 36 " --> pdb=" O THR A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 70 Proline residue: A 62 - end of helix Proline residue: A 67 - end of helix Processing helix chain 'A' and resid 73 through 81 Processing helix chain 'A' and resid 83 through 102 removed outlier: 3.668A pdb=" N LEU A 87 " --> pdb=" O LYS A 83 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TRP A 102 " --> pdb=" O SER A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 117 removed outlier: 3.511A pdb=" N ARG A 107 " --> pdb=" O ASN A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 136 Processing helix chain 'A' and resid 139 through 161 Proline residue: A 149 - end of helix Processing helix chain 'A' and resid 231 through 254 removed outlier: 3.850A pdb=" N THR A 249 " --> pdb=" O ALA A 245 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR A 254 " --> pdb=" O ILE A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 258 Processing helix chain 'A' and resid 259 through 273 Processing helix chain 'A' and resid 280 through 307 Proline residue: A 290 - end of helix Processing helix chain 'A' and resid 323 through 341 removed outlier: 3.527A pdb=" N GLY A 341 " --> pdb=" O TYR A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 364 Processing helix chain 'A' and resid 370 through 376 removed outlier: 3.917A pdb=" N LEU A 375 " --> pdb=" O GLY A 371 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N PHE A 376 " --> pdb=" O TRP A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 396 removed outlier: 3.614A pdb=" N VAL A 388 " --> pdb=" O THR A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 429 removed outlier: 3.652A pdb=" N SER A 429 " --> pdb=" O LYS A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 452 Processing helix chain 'A' and resid 453 through 463 Processing helix chain 'A' and resid 464 through 468 removed outlier: 3.566A pdb=" N SER A 467 " --> pdb=" O PRO A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 485 Processing helix chain 'A' and resid 489 through 508 Proline residue: A 499 - end of helix Proline residue: A 503 - end of helix Processing helix chain 'A' and resid 511 through 524 removed outlier: 3.830A pdb=" N ILE A 515 " --> pdb=" O ASN A 511 " (cutoff:3.500A) Proline residue: A 518 - end of helix removed outlier: 4.180A pdb=" N SER A 524 " --> pdb=" O THR A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 541 Processing helix chain 'A' and resid 546 through 572 Processing helix chain 'A' and resid 573 through 578 Processing helix chain 'B' and resid 3 through 10 Processing helix chain 'B' and resid 10 through 23 removed outlier: 3.588A pdb=" N LEU B 23 " --> pdb=" O THR B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 32 through 51 Processing helix chain 'B' and resid 54 through 61 Processing helix chain 'B' and resid 61 through 69 Proline residue: B 67 - end of helix Processing helix chain 'B' and resid 73 through 81 Processing helix chain 'B' and resid 83 through 102 removed outlier: 3.666A pdb=" N LEU B 87 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TRP B 102 " --> pdb=" O SER B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 117 removed outlier: 3.510A pdb=" N ARG B 107 " --> pdb=" O ASN B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 136 Processing helix chain 'B' and resid 139 through 161 Proline residue: B 149 - end of helix Processing helix chain 'B' and resid 231 through 254 removed outlier: 3.883A pdb=" N THR B 249 " --> pdb=" O ALA B 245 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N THR B 254 " --> pdb=" O ILE B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 258 Processing helix chain 'B' and resid 259 through 273 Processing helix chain 'B' and resid 280 through 307 Proline residue: B 290 - end of helix Processing helix chain 'B' and resid 323 through 341 Processing helix chain 'B' and resid 344 through 364 Processing helix chain 'B' and resid 370 through 376 removed outlier: 3.909A pdb=" N LEU B 375 " --> pdb=" O GLY B 371 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N PHE B 376 " --> pdb=" O TRP B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 396 removed outlier: 3.667A pdb=" N VAL B 388 " --> pdb=" O THR B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 429 removed outlier: 3.651A pdb=" N SER B 429 " --> pdb=" O LYS B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 452 Processing helix chain 'B' and resid 453 through 463 Processing helix chain 'B' and resid 464 through 468 removed outlier: 3.593A pdb=" N SER B 467 " --> pdb=" O PRO B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 485 Processing helix chain 'B' and resid 489 through 508 Proline residue: B 499 - end of helix Proline residue: B 503 - end of helix Processing helix chain 'B' and resid 511 through 524 removed outlier: 3.813A pdb=" N ILE B 515 " --> pdb=" O ASN B 511 " (cutoff:3.500A) Proline residue: B 518 - end of helix removed outlier: 4.138A pdb=" N SER B 524 " --> pdb=" O THR B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 541 Processing helix chain 'B' and resid 546 through 572 Processing helix chain 'B' and resid 573 through 578 546 hydrogen bonds defined for protein. 1626 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.21 Time building geometry restraints manager: 2.33 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: 2307 1.34 - 1.46: 1890 1.46 - 1.58: 3979 1.58 - 1.69: 0 1.69 - 1.81: 88 Bond restraints: 8264 Sorted by residual: bond pdb=" O4 SO4 A 601 " pdb=" S SO4 A 601 " ideal model delta sigma weight residual 1.499 1.458 0.041 2.00e-02 2.50e+03 4.28e+00 bond pdb=" O1 SO4 B 601 " pdb=" S SO4 B 601 " ideal model delta sigma weight residual 1.498 1.457 0.041 2.00e-02 2.50e+03 4.17e+00 bond pdb=" O3 SO4 A 601 " pdb=" S SO4 A 601 " ideal model delta sigma weight residual 1.499 1.458 0.041 2.00e-02 2.50e+03 4.16e+00 bond pdb=" O4 SO4 B 601 " pdb=" S SO4 B 601 " ideal model delta sigma weight residual 1.499 1.458 0.041 2.00e-02 2.50e+03 4.10e+00 bond pdb=" O1 SO4 A 601 " pdb=" S SO4 A 601 " ideal model delta sigma weight residual 1.498 1.458 0.040 2.00e-02 2.50e+03 4.06e+00 ... (remaining 8259 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.38: 10854 1.38 - 2.76: 330 2.76 - 4.14: 68 4.14 - 5.52: 28 5.52 - 6.90: 10 Bond angle restraints: 11290 Sorted by residual: angle pdb=" N VAL A 487 " pdb=" CA VAL A 487 " pdb=" C VAL A 487 " ideal model delta sigma weight residual 112.96 109.62 3.34 1.00e+00 1.00e+00 1.11e+01 angle pdb=" C THR B 286 " pdb=" N PHE B 287 " pdb=" CA PHE B 287 " ideal model delta sigma weight residual 122.54 117.08 5.46 1.65e+00 3.67e-01 1.09e+01 angle pdb=" C THR A 286 " pdb=" N PHE A 287 " pdb=" CA PHE A 287 " ideal model delta sigma weight residual 122.54 117.11 5.43 1.65e+00 3.67e-01 1.08e+01 angle pdb=" N VAL B 487 " pdb=" CA VAL B 487 " pdb=" C VAL B 487 " ideal model delta sigma weight residual 112.96 109.77 3.19 1.00e+00 1.00e+00 1.02e+01 angle pdb=" C ALA A 505 " pdb=" N GLU A 506 " pdb=" CA GLU A 506 " ideal model delta sigma weight residual 122.38 117.20 5.18 1.81e+00 3.05e-01 8.19e+00 ... (remaining 11285 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 4437 17.59 - 35.19: 297 35.19 - 52.78: 40 52.78 - 70.38: 8 70.38 - 87.97: 8 Dihedral angle restraints: 4790 sinusoidal: 1806 harmonic: 2984 Sorted by residual: dihedral pdb=" CA VAL B 29 " pdb=" C VAL B 29 " pdb=" N LEU B 30 " pdb=" CA LEU B 30 " ideal model delta harmonic sigma weight residual 180.00 150.57 29.43 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA VAL A 29 " pdb=" C VAL A 29 " pdb=" N LEU A 30 " pdb=" CA LEU A 30 " ideal model delta harmonic sigma weight residual 180.00 151.01 28.99 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CA ARG A 364 " pdb=" C ARG A 364 " pdb=" N ASP A 365 " pdb=" CA ASP A 365 " ideal model delta harmonic sigma weight residual -180.00 -161.93 -18.07 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 4787 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 779 0.027 - 0.053: 357 0.053 - 0.080: 126 0.080 - 0.106: 67 0.106 - 0.133: 21 Chirality restraints: 1350 Sorted by residual: chirality pdb=" CA GLU B 506 " pdb=" N GLU B 506 " pdb=" C GLU B 506 " pdb=" CB GLU B 506 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.42e-01 chirality pdb=" CA GLU A 506 " pdb=" N GLU A 506 " pdb=" C GLU A 506 " pdb=" CB GLU A 506 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.31e-01 chirality pdb=" CA ILE B 422 " pdb=" N ILE B 422 " pdb=" C ILE B 422 " pdb=" CB ILE B 422 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.06e-01 ... (remaining 1347 not shown) Planarity restraints: 1342 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 24 " -0.035 5.00e-02 4.00e+02 5.30e-02 4.49e+00 pdb=" N PRO A 25 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 25 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 25 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 24 " 0.035 5.00e-02 4.00e+02 5.23e-02 4.37e+00 pdb=" N PRO B 25 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO B 25 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 25 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 26 " -0.028 5.00e-02 4.00e+02 4.26e-02 2.90e+00 pdb=" N PRO A 27 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 27 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 27 " -0.024 5.00e-02 4.00e+02 ... (remaining 1339 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 762 2.74 - 3.28: 8557 3.28 - 3.82: 14094 3.82 - 4.36: 15919 4.36 - 4.90: 28131 Nonbonded interactions: 67463 Sorted by model distance: nonbonded pdb=" O ALA A 59 " pdb=" OH TYR A 81 " model vdw 2.201 3.040 nonbonded pdb=" OD1 ASP B 84 " pdb=" OG SER B 386 " model vdw 2.209 3.040 nonbonded pdb=" NH2 ARG A 107 " pdb=" O GLY A 341 " model vdw 2.267 3.120 nonbonded pdb=" NH2 ARG B 107 " pdb=" O GLY B 341 " model vdw 2.277 3.120 nonbonded pdb=" OH TYR B 268 " pdb=" OE2 GLU B 450 " model vdw 2.302 3.040 ... (remaining 67458 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.680 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: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 21.830 Find NCS groups from input model: 0.140 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 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 0.041 8264 Z= 0.228 Angle : 0.637 6.904 11290 Z= 0.340 Chirality : 0.040 0.133 1350 Planarity : 0.005 0.053 1342 Dihedral : 12.538 87.975 2854 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.36 % Favored : 96.44 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % 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: 1.40 (0.27), residues: 1012 helix: 1.89 (0.19), residues: 748 sheet: None (None), residues: 0 loop : -2.00 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 424 HIS 0.006 0.001 HIS B 509 PHE 0.018 0.001 PHE A 127 TYR 0.006 0.001 TYR A 514 ARG 0.004 0.000 ARG B 344 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.808 Fit side-chains REVERT: A 157 GLN cc_start: 0.7572 (tt0) cc_final: 0.7165 (tt0) REVERT: A 573 ILE cc_start: 0.8816 (mm) cc_final: 0.8542 (mm) REVERT: B 157 GLN cc_start: 0.7574 (tt0) cc_final: 0.7198 (tt0) REVERT: B 234 HIS cc_start: 0.7043 (t-90) cc_final: 0.6822 (t70) REVERT: B 573 ILE cc_start: 0.8807 (mm) cc_final: 0.8535 (mm) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.1580 time to fit residues: 34.0057 Evaluate side-chains 126 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 GLN A 234 HIS A 326 GLN ** A 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 GLN ** B 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.143170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.117365 restraints weight = 12941.777| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.22 r_work: 0.3326 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8264 Z= 0.274 Angle : 0.626 6.711 11290 Z= 0.320 Chirality : 0.042 0.133 1350 Planarity : 0.005 0.051 1342 Dihedral : 4.471 29.486 1064 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.06 % Favored : 96.74 % Rotamer: Outliers : 0.80 % Allowed : 7.50 % Favored : 91.70 % 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: 1.67 (0.27), residues: 1012 helix: 2.06 (0.19), residues: 746 sheet: None (None), residues: 0 loop : -1.76 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 424 HIS 0.004 0.001 HIS B 544 PHE 0.021 0.002 PHE B 287 TYR 0.008 0.001 TYR A 514 ARG 0.003 0.001 ARG B 344 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 138 time to evaluate : 0.817 Fit side-chains REVERT: A 157 GLN cc_start: 0.8124 (tt0) cc_final: 0.7739 (tt0) REVERT: A 326 GLN cc_start: 0.8517 (mt0) cc_final: 0.8247 (mt0) REVERT: A 573 ILE cc_start: 0.8831 (mm) cc_final: 0.8573 (mm) REVERT: B 6 TYR cc_start: 0.6535 (m-80) cc_final: 0.6283 (m-10) REVERT: B 114 MET cc_start: 0.8336 (mtp) cc_final: 0.8114 (mtp) REVERT: B 234 HIS cc_start: 0.7596 (t-90) cc_final: 0.7265 (t70) REVERT: B 573 ILE cc_start: 0.8819 (mm) cc_final: 0.8562 (mm) outliers start: 7 outliers final: 3 residues processed: 141 average time/residue: 0.1635 time to fit residues: 33.3039 Evaluate side-chains 133 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 130 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain B residue 569 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 56 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 76 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 43 optimal weight: 0.2980 chunk 2 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 HIS ** A 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.144254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.118732 restraints weight = 13085.131| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.22 r_work: 0.3353 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8264 Z= 0.203 Angle : 0.576 6.248 11290 Z= 0.293 Chirality : 0.040 0.130 1350 Planarity : 0.005 0.051 1342 Dihedral : 4.384 29.175 1064 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.02 % Allowed : 10.57 % Favored : 88.41 % 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 (0.27), residues: 1012 helix: 2.32 (0.19), residues: 736 sheet: None (None), residues: 0 loop : -1.55 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 424 HIS 0.004 0.001 HIS B 544 PHE 0.018 0.001 PHE B 287 TYR 0.010 0.001 TYR A 514 ARG 0.003 0.001 ARG B 237 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 141 time to evaluate : 0.832 Fit side-chains REVERT: A 157 GLN cc_start: 0.7929 (tt0) cc_final: 0.7645 (tt0) REVERT: A 573 ILE cc_start: 0.8749 (mm) cc_final: 0.8486 (mm) REVERT: B 157 GLN cc_start: 0.7978 (mt0) cc_final: 0.7667 (tt0) REVERT: B 234 HIS cc_start: 0.7376 (t-90) cc_final: 0.7116 (t70) REVERT: B 450 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.6768 (mp0) REVERT: B 573 ILE cc_start: 0.8735 (mm) cc_final: 0.8469 (mm) outliers start: 9 outliers final: 4 residues processed: 149 average time/residue: 0.1614 time to fit residues: 34.9251 Evaluate side-chains 138 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 133 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain B residue 278 CYS Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain B residue 569 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 15 optimal weight: 4.9990 chunk 38 optimal weight: 0.2980 chunk 31 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 HIS A 326 GLN B 325 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.144729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.119582 restraints weight = 12942.492| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.19 r_work: 0.3368 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8264 Z= 0.187 Angle : 0.571 6.550 11290 Z= 0.290 Chirality : 0.040 0.140 1350 Planarity : 0.005 0.049 1342 Dihedral : 4.300 28.553 1064 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.70 % Allowed : 11.48 % Favored : 86.82 % 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 (0.28), residues: 1012 helix: 2.39 (0.19), residues: 738 sheet: None (None), residues: 0 loop : -1.43 (0.39), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 424 HIS 0.004 0.001 HIS A 544 PHE 0.016 0.001 PHE A 287 TYR 0.011 0.001 TYR B 6 ARG 0.002 0.000 ARG B 344 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 139 time to evaluate : 0.904 Fit side-chains revert: symmetry clash REVERT: A 6 TYR cc_start: 0.6603 (m-80) cc_final: 0.6298 (m-10) REVERT: A 450 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.7171 (mm-30) REVERT: A 486 GLU cc_start: 0.6471 (mp0) cc_final: 0.6126 (mp0) REVERT: B 234 HIS cc_start: 0.7519 (t-90) cc_final: 0.7214 (t70) REVERT: B 450 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.7138 (mm-30) outliers start: 15 outliers final: 8 residues processed: 148 average time/residue: 0.1583 time to fit residues: 34.2512 Evaluate side-chains 148 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 138 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 278 CYS Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain B residue 569 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 6 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 83 optimal weight: 0.5980 chunk 71 optimal weight: 9.9990 chunk 101 optimal weight: 0.4980 chunk 87 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 GLN A 234 HIS B 157 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.144726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.119523 restraints weight = 12790.762| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.18 r_work: 0.3370 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8264 Z= 0.193 Angle : 0.569 6.454 11290 Z= 0.287 Chirality : 0.040 0.189 1350 Planarity : 0.005 0.049 1342 Dihedral : 4.244 28.150 1064 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.82 % Allowed : 11.82 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.28), residues: 1012 helix: 2.42 (0.19), residues: 738 sheet: None (None), residues: 0 loop : -1.44 (0.39), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 424 HIS 0.004 0.001 HIS A 544 PHE 0.015 0.001 PHE A 287 TYR 0.010 0.001 TYR B 6 ARG 0.002 0.000 ARG B 237 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 142 time to evaluate : 0.807 Fit side-chains revert: symmetry clash REVERT: A 6 TYR cc_start: 0.6644 (m-80) cc_final: 0.6311 (m-10) REVERT: A 450 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.7159 (mm-30) REVERT: A 486 GLU cc_start: 0.6474 (mp0) cc_final: 0.6003 (mp0) REVERT: A 573 ILE cc_start: 0.8833 (mm) cc_final: 0.8490 (mm) REVERT: A 578 ASP cc_start: 0.7286 (t0) cc_final: 0.6904 (t70) REVERT: B 234 HIS cc_start: 0.7490 (t-90) cc_final: 0.7241 (t70) REVERT: B 268 TYR cc_start: 0.8076 (t80) cc_final: 0.7831 (t80) REVERT: B 347 GLU cc_start: 0.8523 (mt-10) cc_final: 0.8199 (mt-10) REVERT: B 450 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.6893 (mp0) REVERT: B 573 ILE cc_start: 0.8819 (mm) cc_final: 0.8475 (mm) outliers start: 16 outliers final: 9 residues processed: 152 average time/residue: 0.1463 time to fit residues: 32.6597 Evaluate side-chains 152 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 141 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain B residue 569 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 71 optimal weight: 9.9990 chunk 38 optimal weight: 0.3980 chunk 17 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 99 optimal weight: 4.9990 chunk 80 optimal weight: 0.0970 chunk 96 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 GLN A 234 HIS B 157 GLN B 544 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.144877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.119669 restraints weight = 12874.018| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.18 r_work: 0.3368 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8264 Z= 0.191 Angle : 0.573 6.771 11290 Z= 0.289 Chirality : 0.040 0.220 1350 Planarity : 0.005 0.048 1342 Dihedral : 4.231 27.910 1064 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.36 % Allowed : 12.05 % Favored : 86.59 % 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: 2.12 (0.28), residues: 1012 helix: 2.39 (0.19), residues: 744 sheet: None (None), residues: 0 loop : -1.57 (0.39), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 585 HIS 0.004 0.001 HIS B 544 PHE 0.014 0.001 PHE A 287 TYR 0.011 0.001 TYR B 6 ARG 0.002 0.000 ARG B 237 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 142 time to evaluate : 0.892 Fit side-chains REVERT: A 6 TYR cc_start: 0.6597 (m-80) cc_final: 0.6274 (m-10) REVERT: A 148 MET cc_start: 0.8208 (tpt) cc_final: 0.8003 (mmm) REVERT: A 450 GLU cc_start: 0.7415 (OUTLIER) cc_final: 0.7192 (mm-30) REVERT: A 486 GLU cc_start: 0.6450 (mp0) cc_final: 0.5974 (mp0) REVERT: A 573 ILE cc_start: 0.8811 (mm) cc_final: 0.8447 (mm) REVERT: A 578 ASP cc_start: 0.7329 (t0) cc_final: 0.6929 (t70) REVERT: B 268 TYR cc_start: 0.8093 (t80) cc_final: 0.7855 (t80) REVERT: B 347 GLU cc_start: 0.8535 (mt-10) cc_final: 0.8205 (mt-10) REVERT: B 450 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.6906 (mp0) REVERT: B 573 ILE cc_start: 0.8793 (mm) cc_final: 0.8424 (mm) REVERT: B 578 ASP cc_start: 0.7370 (t0) cc_final: 0.6995 (t70) outliers start: 12 outliers final: 8 residues processed: 149 average time/residue: 0.1515 time to fit residues: 33.4111 Evaluate side-chains 145 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 135 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain B residue 569 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 40 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 chunk 82 optimal weight: 0.0470 chunk 13 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 GLN A 234 HIS A 326 GLN A 544 HIS B 157 GLN B 234 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.145266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.119987 restraints weight = 12960.929| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.20 r_work: 0.3371 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8264 Z= 0.186 Angle : 0.563 6.777 11290 Z= 0.285 Chirality : 0.039 0.127 1350 Planarity : 0.005 0.048 1342 Dihedral : 4.195 27.666 1064 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.25 % Allowed : 12.61 % Favored : 86.14 % 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: 2.11 (0.28), residues: 1012 helix: 2.37 (0.19), residues: 744 sheet: None (None), residues: 0 loop : -1.56 (0.39), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 424 HIS 0.005 0.001 HIS A 544 PHE 0.013 0.001 PHE A 287 TYR 0.011 0.001 TYR B 6 ARG 0.002 0.000 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 143 time to evaluate : 0.900 Fit side-chains revert: symmetry clash REVERT: A 347 GLU cc_start: 0.8401 (mt-10) cc_final: 0.8027 (mt-10) REVERT: A 450 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.7025 (mm-30) REVERT: A 486 GLU cc_start: 0.6289 (mp0) cc_final: 0.5890 (mp0) REVERT: A 573 ILE cc_start: 0.8751 (mm) cc_final: 0.8397 (mm) REVERT: A 578 ASP cc_start: 0.7283 (t0) cc_final: 0.6902 (t70) REVERT: B 268 TYR cc_start: 0.7981 (t80) cc_final: 0.7724 (t80) REVERT: B 347 GLU cc_start: 0.8389 (mt-10) cc_final: 0.8028 (mt-10) REVERT: B 450 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.6734 (mp0) REVERT: B 573 ILE cc_start: 0.8732 (mm) cc_final: 0.8380 (mm) REVERT: B 578 ASP cc_start: 0.7265 (t0) cc_final: 0.6910 (t70) outliers start: 11 outliers final: 8 residues processed: 150 average time/residue: 0.1561 time to fit residues: 34.2365 Evaluate side-chains 144 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 134 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain B residue 569 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 10 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 67 optimal weight: 6.9990 chunk 31 optimal weight: 0.5980 chunk 88 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 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 157 GLN A 234 HIS A 509 HIS B 157 GLN B 234 HIS B 509 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.143940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.118190 restraints weight = 13026.065| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.21 r_work: 0.3342 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8264 Z= 0.239 Angle : 0.600 6.860 11290 Z= 0.303 Chirality : 0.041 0.266 1350 Planarity : 0.005 0.048 1342 Dihedral : 4.294 28.022 1064 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.48 % Allowed : 12.50 % Favored : 86.02 % 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: 2.01 (0.28), residues: 1012 helix: 2.30 (0.19), residues: 744 sheet: None (None), residues: 0 loop : -1.57 (0.39), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 424 HIS 0.016 0.003 HIS B 509 PHE 0.014 0.001 PHE A 287 TYR 0.017 0.001 TYR A 6 ARG 0.003 0.000 ARG B 237 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 131 time to evaluate : 0.869 Fit side-chains REVERT: A 345 TYR cc_start: 0.5457 (m-80) cc_final: 0.5232 (m-80) REVERT: A 450 GLU cc_start: 0.7289 (OUTLIER) cc_final: 0.7053 (mm-30) REVERT: A 573 ILE cc_start: 0.8766 (mm) cc_final: 0.8395 (mm) REVERT: A 578 ASP cc_start: 0.7391 (t0) cc_final: 0.6914 (t70) REVERT: B 243 CYS cc_start: 0.8600 (p) cc_final: 0.8184 (p) REVERT: B 268 TYR cc_start: 0.8025 (t80) cc_final: 0.7615 (t80) REVERT: B 529 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7921 (mt) REVERT: B 573 ILE cc_start: 0.8747 (mm) cc_final: 0.8383 (mm) REVERT: B 578 ASP cc_start: 0.7403 (t0) cc_final: 0.6963 (t70) outliers start: 13 outliers final: 10 residues processed: 143 average time/residue: 0.1525 time to fit residues: 32.3872 Evaluate side-chains 142 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 509 HIS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 569 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 37 optimal weight: 2.9990 chunk 21 optimal weight: 0.1980 chunk 73 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 61 optimal weight: 0.0570 chunk 85 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 35 optimal weight: 0.0470 chunk 58 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 GLN A 234 HIS A 509 HIS B 157 GLN B 234 HIS B 509 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.146090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.120613 restraints weight = 13113.592| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.22 r_work: 0.3378 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8264 Z= 0.177 Angle : 0.581 7.396 11290 Z= 0.295 Chirality : 0.040 0.275 1350 Planarity : 0.005 0.048 1342 Dihedral : 4.240 27.555 1064 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.82 % Allowed : 12.95 % Favored : 85.23 % 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: 2.07 (0.28), residues: 1012 helix: 2.33 (0.19), residues: 744 sheet: None (None), residues: 0 loop : -1.51 (0.39), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 424 HIS 0.021 0.003 HIS B 509 PHE 0.016 0.001 PHE A 3 TYR 0.020 0.001 TYR A 6 ARG 0.003 0.000 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 145 time to evaluate : 0.893 Fit side-chains REVERT: A 347 GLU cc_start: 0.8383 (mt-10) cc_final: 0.7988 (mt-10) REVERT: A 450 GLU cc_start: 0.7223 (OUTLIER) cc_final: 0.6999 (mm-30) REVERT: A 573 ILE cc_start: 0.8735 (mm) cc_final: 0.8375 (mm) REVERT: A 578 ASP cc_start: 0.7394 (t0) cc_final: 0.6902 (t0) REVERT: B 243 CYS cc_start: 0.8649 (p) cc_final: 0.8183 (p) REVERT: B 347 GLU cc_start: 0.8383 (mt-10) cc_final: 0.7975 (mt-10) REVERT: B 450 GLU cc_start: 0.7247 (OUTLIER) cc_final: 0.7004 (mm-30) REVERT: B 529 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7911 (mt) REVERT: B 573 ILE cc_start: 0.8686 (mm) cc_final: 0.8338 (mm) REVERT: B 578 ASP cc_start: 0.7408 (t0) cc_final: 0.6931 (t70) outliers start: 16 outliers final: 12 residues processed: 155 average time/residue: 0.1510 time to fit residues: 34.7897 Evaluate side-chains 152 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 137 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 509 HIS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 569 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 9 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 96 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 80 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 HIS ** A 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 GLN ** B 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.145120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.119680 restraints weight = 12796.177| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.17 r_work: 0.3368 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8264 Z= 0.207 Angle : 0.609 15.615 11290 Z= 0.303 Chirality : 0.041 0.272 1350 Planarity : 0.005 0.048 1342 Dihedral : 4.276 27.617 1064 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.59 % Allowed : 13.64 % Favored : 84.77 % 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: 2.03 (0.28), residues: 1012 helix: 2.28 (0.19), residues: 744 sheet: None (None), residues: 0 loop : -1.46 (0.39), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 424 HIS 0.011 0.002 HIS B 509 PHE 0.018 0.001 PHE A 3 TYR 0.021 0.001 TYR A 6 ARG 0.003 0.000 ARG A 237 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 136 time to evaluate : 0.804 Fit side-chains REVERT: A 450 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.7176 (mm-30) REVERT: A 573 ILE cc_start: 0.8802 (mm) cc_final: 0.8429 (mm) REVERT: A 578 ASP cc_start: 0.7535 (t0) cc_final: 0.7002 (t0) REVERT: B 243 CYS cc_start: 0.8812 (p) cc_final: 0.8350 (p) REVERT: B 347 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8198 (mt-10) REVERT: B 450 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.7180 (mm-30) REVERT: B 529 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7935 (mt) REVERT: B 573 ILE cc_start: 0.8749 (mm) cc_final: 0.8367 (mm) REVERT: B 578 ASP cc_start: 0.7576 (t0) cc_final: 0.6999 (t70) outliers start: 14 outliers final: 11 residues processed: 147 average time/residue: 0.1475 time to fit residues: 32.0249 Evaluate side-chains 148 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 134 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 569 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 28 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 68 optimal weight: 0.6980 chunk 73 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 76 optimal weight: 20.0000 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 HIS A 509 HIS B 234 HIS B 509 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.144079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.118432 restraints weight = 12933.585| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.19 r_work: 0.3349 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8264 Z= 0.226 Angle : 0.624 15.479 11290 Z= 0.310 Chirality : 0.041 0.267 1350 Planarity : 0.005 0.047 1342 Dihedral : 4.304 27.954 1064 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.82 % Allowed : 13.75 % Favored : 84.43 % 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: 1.98 (0.28), residues: 1012 helix: 2.25 (0.19), residues: 744 sheet: None (None), residues: 0 loop : -1.48 (0.39), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 424 HIS 0.014 0.003 HIS A 509 PHE 0.018 0.001 PHE A 3 TYR 0.021 0.001 TYR A 6 ARG 0.003 0.000 ARG A 237 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4014.32 seconds wall clock time: 70 minutes 13.56 seconds (4213.56 seconds total)