Starting phenix.real_space_refine on Fri Aug 22 21:15:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y5x_38955/08_2025/8y5x_38955.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y5x_38955/08_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_38955/08_2025/8y5x_38955.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y5x_38955/08_2025/8y5x_38955.map" model { file = "/net/cci-nas-00/data/ceres_data/8y5x_38955/08_2025/8y5x_38955.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y5x_38955/08_2025/8y5x_38955.cif" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.23, per 1000 atoms: 0.28 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: 0.72 Conformation dependent library (CDL) restraints added in 433.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.28 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: 1.36 Time building geometry restraints manager: 0.89 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: 0.02 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: 2.160 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.630 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.440 ------------------------------------------------------------------------------- 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= 0.158 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.000 ARG B 344 TYR 0.006 0.001 TYR A 514 PHE 0.018 0.001 PHE A 127 TRP 0.008 0.001 TRP B 424 HIS 0.006 0.001 HIS B 509 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 8264) covalent geometry : angle 0.63657 (11290) hydrogen bonds : bond 0.11632 ( 546) hydrogen bonds : angle 4.85591 ( 1626) *********************** 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 : 0.339 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: 0.7194 (tt0) REVERT: B 234 HIS cc_start: 0.7043 (t-90) cc_final: 0.6821 (t70) REVERT: B 573 ILE cc_start: 0.8807 (mm) cc_final: 0.8536 (mm) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.0766 time to fit residues: 16.7436 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 : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** B 544 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.142465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.116549 restraints weight = 12930.756| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.22 r_work: 0.3319 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8264 Z= 0.194 Angle : 0.643 6.926 11290 Z= 0.329 Chirality : 0.042 0.133 1350 Planarity : 0.006 0.052 1342 Dihedral : 4.514 29.623 1064 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.91 % Allowed : 7.27 % Favored : 91.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.63 (0.27), residues: 1012 helix: 2.02 (0.19), residues: 746 sheet: None (None), residues: 0 loop : -1.76 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 107 TYR 0.009 0.001 TYR A 514 PHE 0.021 0.002 PHE B 287 TRP 0.009 0.001 TRP A 424 HIS 0.004 0.001 HIS B 544 Details of bonding type rmsd covalent geometry : bond 0.00466 ( 8264) covalent geometry : angle 0.64315 (11290) hydrogen bonds : bond 0.04895 ( 546) hydrogen bonds : angle 4.16880 ( 1626) *********************** 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: 8 poor density : 137 time to evaluate : 0.339 Fit side-chains REVERT: A 114 MET cc_start: 0.8321 (mtp) cc_final: 0.8114 (mtp) REVERT: A 157 GLN cc_start: 0.8136 (tt0) cc_final: 0.7748 (tt0) REVERT: A 326 GLN cc_start: 0.8507 (mt0) cc_final: 0.8257 (mt0) REVERT: A 573 ILE cc_start: 0.8834 (mm) cc_final: 0.8568 (mm) REVERT: B 6 TYR cc_start: 0.6534 (m-80) cc_final: 0.6286 (m-10) REVERT: B 234 HIS cc_start: 0.7606 (t-90) cc_final: 0.7264 (t70) REVERT: B 573 ILE cc_start: 0.8826 (mm) cc_final: 0.8560 (mm) outliers start: 8 outliers final: 4 residues processed: 140 average time/residue: 0.0791 time to fit residues: 16.1235 Evaluate side-chains 132 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 128 time to evaluate : 0.278 ------------------------------------------------------------------------------- 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 569 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 38 optimal weight: 0.9990 chunk 101 optimal weight: 0.0970 chunk 72 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 29 optimal weight: 6.9990 chunk 89 optimal weight: 0.1980 chunk 39 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 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 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 = 0.3809 r_free = 0.3809 target = 0.145249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.119940 restraints weight = 12837.323| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.19 r_work: 0.3369 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1176 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= 0.126 Angle : 0.568 6.169 11290 Z= 0.290 Chirality : 0.039 0.129 1350 Planarity : 0.005 0.051 1342 Dihedral : 4.361 29.193 1064 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.14 % Allowed : 10.23 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.02 (0.27), residues: 1012 helix: 2.32 (0.19), residues: 738 sheet: None (None), residues: 0 loop : -1.53 (0.39), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 107 TYR 0.010 0.001 TYR A 514 PHE 0.019 0.001 PHE B 287 TRP 0.010 0.001 TRP B 572 HIS 0.003 0.001 HIS B 544 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 8264) covalent geometry : angle 0.56787 (11290) hydrogen bonds : bond 0.04123 ( 546) hydrogen bonds : angle 3.88796 ( 1626) *********************** 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 152 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 142 time to evaluate : 0.324 Fit side-chains REVERT: A 114 MET cc_start: 0.8291 (mtp) cc_final: 0.7987 (mtp) REVERT: A 157 GLN cc_start: 0.8034 (tt0) cc_final: 0.7727 (tt0) REVERT: A 450 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.7193 (mm-30) REVERT: A 573 ILE cc_start: 0.8793 (mm) cc_final: 0.8529 (mm) REVERT: B 6 TYR cc_start: 0.6551 (m-80) cc_final: 0.6300 (m-10) REVERT: B 157 GLN cc_start: 0.8097 (mt0) cc_final: 0.7704 (tt0) REVERT: B 234 HIS cc_start: 0.7565 (t-90) cc_final: 0.7266 (t70) REVERT: B 450 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.7106 (mm-30) REVERT: B 573 ILE cc_start: 0.8772 (mm) cc_final: 0.8506 (mm) outliers start: 10 outliers final: 4 residues processed: 151 average time/residue: 0.0711 time to fit residues: 16.1101 Evaluate side-chains 136 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 130 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain A residue 569 ILE 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 2 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 67 optimal weight: 0.7980 chunk 49 optimal weight: 7.9990 chunk 71 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 25 optimal weight: 9.9990 chunk 78 optimal weight: 0.8980 chunk 98 optimal weight: 0.0270 chunk 76 optimal weight: 6.9990 overall best weight: 1.1442 ------------------------------------------------------------------------------- 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 ** A 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 HIS B 325 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 = 0.3783 r_free = 0.3783 target = 0.142806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.117261 restraints weight = 13173.646| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.21 r_work: 0.3325 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8264 Z= 0.160 Angle : 0.598 6.664 11290 Z= 0.302 Chirality : 0.041 0.129 1350 Planarity : 0.005 0.050 1342 Dihedral : 4.408 28.986 1064 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.36 % Allowed : 11.70 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.02 (0.27), residues: 1012 helix: 2.33 (0.19), residues: 736 sheet: None (None), residues: 0 loop : -1.54 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 344 TYR 0.009 0.001 TYR A 514 PHE 0.016 0.001 PHE A 287 TRP 0.009 0.001 TRP B 585 HIS 0.004 0.001 HIS A 544 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 8264) covalent geometry : angle 0.59782 (11290) hydrogen bonds : bond 0.04388 ( 546) hydrogen bonds : angle 3.90628 ( 1626) *********************** 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 150 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 138 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: A 6 TYR cc_start: 0.6459 (m-80) cc_final: 0.6229 (m-10) REVERT: A 345 TYR cc_start: 0.5491 (m-80) cc_final: 0.5269 (m-80) REVERT: B 234 HIS cc_start: 0.7364 (t-90) cc_final: 0.7075 (t70) outliers start: 12 outliers final: 5 residues processed: 147 average time/residue: 0.0785 time to fit residues: 16.7501 Evaluate side-chains 140 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 135 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain B residue 256 ILE 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 49 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 6 optimal weight: 0.1980 chunk 34 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 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 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 = 0.3802 r_free = 0.3802 target = 0.144425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.118990 restraints weight = 12966.908| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.19 r_work: 0.3355 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1535 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= 0.128 Angle : 0.570 6.486 11290 Z= 0.287 Chirality : 0.040 0.207 1350 Planarity : 0.005 0.050 1342 Dihedral : 4.300 28.481 1064 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.36 % Allowed : 11.59 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.12 (0.27), residues: 1012 helix: 2.39 (0.19), residues: 738 sheet: None (None), residues: 0 loop : -1.49 (0.39), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 11 TYR 0.007 0.001 TYR A 514 PHE 0.015 0.001 PHE B 287 TRP 0.010 0.001 TRP B 572 HIS 0.003 0.001 HIS A 544 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 8264) covalent geometry : angle 0.57027 (11290) hydrogen bonds : bond 0.04001 ( 546) hydrogen bonds : angle 3.82010 ( 1626) *********************** 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 154 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 142 time to evaluate : 0.294 Fit side-chains REVERT: A 6 TYR cc_start: 0.6497 (m-80) cc_final: 0.6235 (m-10) REVERT: A 450 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.6998 (mm-30) REVERT: A 486 GLU cc_start: 0.6327 (mp0) cc_final: 0.5904 (mp0) REVERT: A 573 ILE cc_start: 0.8784 (mm) cc_final: 0.8433 (mm) REVERT: A 578 ASP cc_start: 0.7168 (t0) cc_final: 0.6819 (t70) REVERT: B 234 HIS cc_start: 0.7316 (t-90) cc_final: 0.7099 (t70) REVERT: B 268 TYR cc_start: 0.7938 (t80) cc_final: 0.7686 (t80) REVERT: B 347 GLU cc_start: 0.8367 (mt-10) cc_final: 0.8010 (mt-10) REVERT: B 450 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6719 (mp0) REVERT: B 573 ILE cc_start: 0.8771 (mm) cc_final: 0.8422 (mm) outliers start: 12 outliers final: 6 residues processed: 151 average time/residue: 0.0731 time to fit residues: 16.4570 Evaluate side-chains 147 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 139 time to evaluate : 0.367 ------------------------------------------------------------------------------- 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 278 CYS Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain B residue 28 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 36 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 50 optimal weight: 0.0670 chunk 12 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 overall best weight: 0.6518 ------------------------------------------------------------------------------- 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 = 0.3806 r_free = 0.3806 target = 0.144833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.119463 restraints weight = 12992.730| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.19 r_work: 0.3360 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1618 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= 0.127 Angle : 0.561 6.778 11290 Z= 0.284 Chirality : 0.039 0.129 1350 Planarity : 0.005 0.049 1342 Dihedral : 4.234 28.102 1064 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.02 % Allowed : 12.27 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.09 (0.27), residues: 1012 helix: 2.38 (0.19), residues: 744 sheet: None (None), residues: 0 loop : -1.63 (0.39), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 237 TYR 0.007 0.001 TYR A 379 PHE 0.014 0.001 PHE A 287 TRP 0.015 0.001 TRP A 585 HIS 0.003 0.001 HIS B 544 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 8264) covalent geometry : angle 0.56083 (11290) hydrogen bonds : bond 0.03956 ( 546) hydrogen bonds : angle 3.76188 ( 1626) *********************** 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 150 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 141 time to evaluate : 0.327 Fit side-chains revert: symmetry clash REVERT: A 6 TYR cc_start: 0.6598 (m-80) cc_final: 0.6282 (m-10) REVERT: A 450 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.7171 (mm-30) REVERT: A 573 ILE cc_start: 0.8808 (mm) cc_final: 0.8437 (mm) REVERT: A 578 ASP cc_start: 0.7387 (t0) cc_final: 0.6966 (t70) REVERT: B 268 TYR cc_start: 0.8065 (t80) cc_final: 0.7819 (t80) REVERT: B 450 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.6876 (mp0) REVERT: B 573 ILE cc_start: 0.8797 (mm) cc_final: 0.8422 (mm) REVERT: B 578 ASP cc_start: 0.7323 (t0) cc_final: 0.6941 (t70) outliers start: 9 outliers final: 6 residues processed: 150 average time/residue: 0.0732 time to fit residues: 16.4097 Evaluate side-chains 144 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 136 time to evaluate : 0.329 ------------------------------------------------------------------------------- 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 450 GLU 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 45 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 81 optimal weight: 0.6980 chunk 76 optimal weight: 9.9990 chunk 60 optimal weight: 1.9990 chunk 85 optimal weight: 0.4980 chunk 101 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 GLN A 234 HIS A 544 HIS B 157 GLN B 234 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.142786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.117062 restraints weight = 12983.414| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.19 r_work: 0.3328 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8264 Z= 0.162 Angle : 0.592 6.903 11290 Z= 0.299 Chirality : 0.041 0.212 1350 Planarity : 0.005 0.047 1342 Dihedral : 4.336 28.491 1064 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.36 % Allowed : 12.73 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.93 (0.27), residues: 1012 helix: 2.21 (0.19), residues: 754 sheet: None (None), residues: 0 loop : -1.67 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 344 TYR 0.008 0.001 TYR B 514 PHE 0.015 0.001 PHE B 287 TRP 0.009 0.001 TRP A 585 HIS 0.004 0.001 HIS B 234 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 8264) covalent geometry : angle 0.59192 (11290) hydrogen bonds : bond 0.04274 ( 546) hydrogen bonds : angle 3.84041 ( 1626) *********************** 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 149 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 137 time to evaluate : 0.359 Fit side-chains REVERT: A 6 TYR cc_start: 0.6494 (m-80) cc_final: 0.6238 (m-10) REVERT: A 345 TYR cc_start: 0.5767 (m-80) cc_final: 0.5557 (m-80) REVERT: A 573 ILE cc_start: 0.8836 (mm) cc_final: 0.8474 (mm) REVERT: A 578 ASP cc_start: 0.7532 (t0) cc_final: 0.7047 (t70) REVERT: B 243 CYS cc_start: 0.8757 (p) cc_final: 0.8317 (p) REVERT: B 268 TYR cc_start: 0.8098 (t80) cc_final: 0.7821 (t80) REVERT: B 450 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.6929 (mp0) REVERT: B 529 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7924 (mt) REVERT: B 573 ILE cc_start: 0.8819 (mm) cc_final: 0.8453 (mm) REVERT: B 578 ASP cc_start: 0.7529 (t0) cc_final: 0.7057 (t70) outliers start: 12 outliers final: 7 residues processed: 146 average time/residue: 0.0782 time to fit residues: 16.7046 Evaluate side-chains 145 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 136 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain B residue 256 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 97 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 69 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 35 optimal weight: 0.0470 chunk 38 optimal weight: 0.0770 overall best weight: 0.4836 ------------------------------------------------------------------------------- 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 544 HIS B 157 GLN B 234 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.145005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.119762 restraints weight = 12908.578| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.19 r_work: 0.3369 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1785 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= 0.123 Angle : 0.568 6.789 11290 Z= 0.286 Chirality : 0.039 0.127 1350 Planarity : 0.005 0.048 1342 Dihedral : 4.228 27.905 1064 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.25 % Allowed : 13.30 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.05 (0.27), residues: 1012 helix: 2.32 (0.19), residues: 750 sheet: None (None), residues: 0 loop : -1.64 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 237 TYR 0.013 0.001 TYR A 268 PHE 0.013 0.001 PHE B 287 TRP 0.010 0.001 TRP A 424 HIS 0.005 0.001 HIS A 544 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 8264) covalent geometry : angle 0.56776 (11290) hydrogen bonds : bond 0.03892 ( 546) hydrogen bonds : angle 3.78157 ( 1626) *********************** 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 160 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 149 time to evaluate : 0.274 Fit side-chains REVERT: A 6 TYR cc_start: 0.6498 (m-80) cc_final: 0.6233 (m-10) REVERT: A 573 ILE cc_start: 0.8783 (mm) cc_final: 0.8443 (mm) REVERT: A 578 ASP cc_start: 0.7528 (t0) cc_final: 0.7007 (t70) REVERT: B 243 CYS cc_start: 0.8800 (p) cc_final: 0.8328 (p) REVERT: B 268 TYR cc_start: 0.8080 (t80) cc_final: 0.7690 (t80) REVERT: B 450 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.7018 (mm-30) REVERT: B 529 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7910 (mt) REVERT: B 573 ILE cc_start: 0.8778 (mm) cc_final: 0.8430 (mm) REVERT: B 578 ASP cc_start: 0.7514 (t0) cc_final: 0.7023 (t70) outliers start: 11 outliers final: 8 residues processed: 158 average time/residue: 0.0728 time to fit residues: 17.1511 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 : 0.316 ------------------------------------------------------------------------------- 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 278 CYS 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 60 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 23 optimal weight: 0.0970 chunk 78 optimal weight: 0.0970 chunk 75 optimal weight: 0.0970 chunk 98 optimal weight: 8.9990 overall best weight: 0.3974 ------------------------------------------------------------------------------- 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 509 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.146422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.121348 restraints weight = 12921.485| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.19 r_work: 0.3388 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1902 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= 0.120 Angle : 0.576 7.579 11290 Z= 0.294 Chirality : 0.040 0.284 1350 Planarity : 0.005 0.048 1342 Dihedral : 4.163 27.582 1064 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.48 % Allowed : 13.18 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.03 (0.28), residues: 1012 helix: 2.30 (0.19), residues: 750 sheet: None (None), residues: 0 loop : -1.64 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 237 TYR 0.012 0.001 TYR B 514 PHE 0.011 0.001 PHE A 287 TRP 0.010 0.001 TRP B 424 HIS 0.019 0.003 HIS B 509 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 8264) covalent geometry : angle 0.57617 (11290) hydrogen bonds : bond 0.03747 ( 546) hydrogen bonds : angle 3.78778 ( 1626) *********************** 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 157 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 144 time to evaluate : 0.336 Fit side-chains REVERT: A 573 ILE cc_start: 0.8694 (mm) cc_final: 0.8344 (mm) REVERT: A 578 ASP cc_start: 0.7397 (t0) cc_final: 0.6876 (t0) REVERT: B 268 TYR cc_start: 0.7962 (t80) cc_final: 0.7543 (t80) REVERT: B 347 GLU cc_start: 0.8389 (mt-10) cc_final: 0.7965 (mt-10) REVERT: B 450 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.6870 (mm-30) REVERT: B 529 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7908 (mt) REVERT: B 573 ILE cc_start: 0.8687 (mm) cc_final: 0.8340 (mm) REVERT: B 578 ASP cc_start: 0.7337 (t0) cc_final: 0.6841 (t70) outliers start: 13 outliers final: 11 residues processed: 154 average time/residue: 0.0706 time to fit residues: 16.3073 Evaluate side-chains 158 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 145 time to evaluate : 0.314 ------------------------------------------------------------------------------- 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 278 CYS Chi-restraints excluded: chain A residue 297 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 332 VAL 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 16 optimal weight: 6.9990 chunk 85 optimal weight: 0.0270 chunk 53 optimal weight: 0.9980 chunk 62 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 95 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 83 optimal weight: 0.8980 overall best weight: 0.6238 ------------------------------------------------------------------------------- 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 509 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.145989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.120644 restraints weight = 12954.185| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.21 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: 0.8285 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8264 Z= 0.131 Angle : 0.611 15.238 11290 Z= 0.303 Chirality : 0.041 0.283 1350 Planarity : 0.005 0.047 1342 Dihedral : 4.188 27.672 1064 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.59 % Allowed : 13.52 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.99 (0.27), residues: 1012 helix: 2.26 (0.19), residues: 750 sheet: None (None), residues: 0 loop : -1.60 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 237 TYR 0.023 0.001 TYR A 6 PHE 0.012 0.001 PHE A 287 TRP 0.009 0.001 TRP B 424 HIS 0.012 0.002 HIS B 509 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 8264) covalent geometry : angle 0.61067 (11290) hydrogen bonds : bond 0.03836 ( 546) hydrogen bonds : angle 3.81323 ( 1626) ********************** 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 149 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 135 time to evaluate : 0.316 Fit side-chains REVERT: A 573 ILE cc_start: 0.8704 (mm) cc_final: 0.8323 (mm) REVERT: A 578 ASP cc_start: 0.7397 (t0) cc_final: 0.6861 (t0) REVERT: B 268 TYR cc_start: 0.7972 (t80) cc_final: 0.7686 (t80) REVERT: B 450 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.6728 (mp0) REVERT: B 529 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7917 (mt) REVERT: B 573 ILE cc_start: 0.8692 (mm) cc_final: 0.8317 (mm) REVERT: B 578 ASP cc_start: 0.7393 (t0) cc_final: 0.6846 (t70) outliers start: 14 outliers final: 11 residues processed: 146 average time/residue: 0.0713 time to fit residues: 15.6453 Evaluate side-chains 149 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 136 time to evaluate : 0.320 ------------------------------------------------------------------------------- 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 278 CYS Chi-restraints excluded: chain A residue 297 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 332 VAL 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 73 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 97 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 = 0.3804 r_free = 0.3804 target = 0.144540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.118972 restraints weight = 12786.458| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.19 r_work: 0.3355 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8264 Z= 0.153 Angle : 0.626 15.382 11290 Z= 0.311 Chirality : 0.042 0.279 1350 Planarity : 0.005 0.046 1342 Dihedral : 4.273 27.937 1064 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.48 % Allowed : 13.86 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.93 (0.27), residues: 1012 helix: 2.21 (0.19), residues: 750 sheet: None (None), residues: 0 loop : -1.60 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 237 TYR 0.023 0.001 TYR A 6 PHE 0.013 0.001 PHE A 287 TRP 0.009 0.001 TRP A 424 HIS 0.009 0.002 HIS B 509 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 8264) covalent geometry : angle 0.62591 (11290) hydrogen bonds : bond 0.04046 ( 546) hydrogen bonds : angle 3.86688 ( 1626) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2032.93 seconds wall clock time: 35 minutes 42.55 seconds (2142.55 seconds total)