Starting phenix.real_space_refine on Thu Jul 2 08:54:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y5x_38955/07_2026/8y5x_38955.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y5x_38955/07_2026/8y5x_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 { model { file = "/net/cci-nas-00/data/ceres_data/8y5x_38955/07_2026/8y5x_38955.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y5x_38955/07_2026/8y5x_38955.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8y5x_38955/07_2026/8y5x_38955.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y5x_38955/07_2026/8y5x_38955.map" } 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-dev-6108/lib/python3.11/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, 5 Ad-hoc single atom residues: {' NA': 1} Unusual residues: {'SO4': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 5 Ad-hoc single atom residues: {' NA': 1} Unusual residues: {'SO4': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Time building chain proxies: 1.93, per 1000 atoms: 0.24 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: 0.77 Conformation dependent library (CDL) restraints added in 433.6 milliseconds 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: 0.23 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: 1.31 Time building geometry restraints manager: 1.02 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: 2.030 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: 0.040 Process input model: 9.210 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 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 are 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/Z covalent geometry : bond 0.00348 / 0.16 ( 8264) covalent geometry : angle 0.63657 / 0.34 (11290) hydrogen bonds : bond 0.11632 / 7.29 ( 546) hydrogen bonds : angle 4.85591 / 3.53 ( 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 : 0.304 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: 0.0775 time to fit residues: 17.0484 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 : 0.313 ------------------------------------------------------------------------------- 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... 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 = 0.142489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.116602 restraints weight = 12926.648| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.21 r_work: 0.3314 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1059 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 : 0.642 6.916 11290 Z= 0.328 Chirality : 0.042 0.133 1350 Planarity : 0.006 0.052 1342 Dihedral : 4.516 29.689 1064 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.91 % Allowed : 7.50 % Favored : 91.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.27), residues: 1012 helix: 2.01 (0.19), residues: 746 sheet: None (None), residues: 0 loop : -1.79 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 344 TYR 0.009 0.001 TYR A 514 PHE 0.022 0.002 PHE B 287 TRP 0.009 0.001 TRP A 424 HIS 0.003 0.001 HIS B 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.19 ( 8264) covalent geometry : angle 0.64233 / 0.33 (11290) hydrogen bonds : bond 0.04905 / 3.18 ( 546) hydrogen bonds : angle 4.16143 / 2.99 ( 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 : 0.390 Fit side-chains REVERT: A 114 MET cc_start: 0.8200 (mtp) cc_final: 0.7989 (mtp) REVERT: A 157 GLN cc_start: 0.8044 (tt0) cc_final: 0.7668 (tt0) REVERT: A 573 ILE cc_start: 0.8782 (mm) cc_final: 0.8538 (mm) REVERT: B 234 HIS cc_start: 0.7432 (t-90) cc_final: 0.7121 (t70) REVERT: B 573 ILE cc_start: 0.8764 (mm) cc_final: 0.8497 (mm) outliers start: 8 outliers final: 4 residues processed: 140 average time/residue: 0.0778 time to fit residues: 15.9136 Evaluate side-chains 133 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 129 time to evaluate : 0.316 ------------------------------------------------------------------------------- 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: 0.7980 chunk 72 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 29 optimal weight: 5.9990 chunk 89 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 234 HIS A 326 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.143911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.118450 restraints weight = 12825.588| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.20 r_work: 0.3348 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1199 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= 0.142 Angle : 0.584 6.296 11290 Z= 0.298 Chirality : 0.040 0.130 1350 Planarity : 0.005 0.051 1342 Dihedral : 4.422 29.378 1064 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.02 % Allowed : 10.80 % Favored : 88.18 % 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 are not related in a simple way. whole: 1.92 (0.27), residues: 1012 helix: 2.27 (0.19), residues: 736 sheet: None (None), residues: 0 loop : -1.61 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 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 0.004 0.001 HIS B 544 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 ( 8264) covalent geometry : angle 0.58376 / 0.30 (11290) hydrogen bonds : bond 0.04377 / 2.82 ( 546) hydrogen bonds : angle 3.96399 / 2.84 ( 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 149 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 140 time to evaluate : 0.304 Fit side-chains REVERT: A 114 MET cc_start: 0.8309 (mtp) cc_final: 0.8000 (mtp) REVERT: A 157 GLN cc_start: 0.8070 (tt0) cc_final: 0.7761 (tt0) REVERT: A 326 GLN cc_start: 0.8563 (mt0) cc_final: 0.8264 (mt0) REVERT: A 573 ILE cc_start: 0.8819 (mm) cc_final: 0.8553 (mm) REVERT: B 157 GLN cc_start: 0.8117 (mt0) cc_final: 0.7758 (tt0) REVERT: B 234 HIS cc_start: 0.7620 (t-90) cc_final: 0.7303 (t70) REVERT: B 450 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.7008 (mp0) REVERT: B 573 ILE cc_start: 0.8803 (mm) cc_final: 0.8534 (mm) outliers start: 9 outliers final: 4 residues processed: 146 average time/residue: 0.0710 time to fit residues: 15.3291 Evaluate side-chains 137 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 132 time to evaluate : 0.313 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 49 optimal weight: 5.9990 chunk 71 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 98 optimal weight: 6.9990 chunk 76 optimal weight: 0.6980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 234 HIS ** A 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 GLN ** B 536 ASN ** 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 = 0.3785 r_free = 0.3785 target = 0.143074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.117287 restraints weight = 13166.438| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.22 r_work: 0.3332 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1394 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= 0.156 Angle : 0.599 6.633 11290 Z= 0.301 Chirality : 0.041 0.138 1350 Planarity : 0.005 0.050 1342 Dihedral : 4.420 29.149 1064 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.48 % Allowed : 12.05 % Favored : 86.48 % 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 are not related in a simple way. whole: 1.96 (0.27), residues: 1012 helix: 2.24 (0.19), residues: 742 sheet: None (None), residues: 0 loop : -1.49 (0.39), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 237 TYR 0.009 0.001 TYR A 514 PHE 0.016 0.001 PHE B 287 TRP 0.009 0.001 TRP B 572 HIS 0.003 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 ( 8264) covalent geometry : angle 0.59949 / 0.30 (11290) hydrogen bonds : bond 0.04343 / 2.81 ( 546) hydrogen bonds : angle 3.91976 / 2.81 ( 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 149 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 136 time to evaluate : 0.304 Fit side-chains REVERT: A 6 TYR cc_start: 0.6450 (m-80) cc_final: 0.6230 (m-10) REVERT: A 157 GLN cc_start: 0.7914 (tt0) cc_final: 0.7693 (tt0) REVERT: A 345 TYR cc_start: 0.5537 (m-80) cc_final: 0.5317 (m-80) REVERT: A 450 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.7077 (mm-30) REVERT: B 234 HIS cc_start: 0.7338 (t-90) cc_final: 0.7052 (t70) outliers start: 13 outliers final: 7 residues processed: 145 average time/residue: 0.0698 time to fit residues: 14.9376 Evaluate side-chains 140 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 132 time to evaluate : 0.302 ------------------------------------------------------------------------------- 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 569 ILE Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 278 CYS 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: 0.8980 chunk 12 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 234 HIS A 326 GLN A 544 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.143747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.118086 restraints weight = 12963.184| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.21 r_work: 0.3346 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1503 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= 0.136 Angle : 0.580 6.534 11290 Z= 0.292 Chirality : 0.040 0.179 1350 Planarity : 0.005 0.050 1342 Dihedral : 4.342 28.751 1064 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.82 % Allowed : 11.25 % 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 are not related in a simple way. whole: 2.07 (0.27), residues: 1012 helix: 2.35 (0.19), residues: 738 sheet: None (None), residues: 0 loop : -1.50 (0.39), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 344 TYR 0.009 0.001 TYR B 6 PHE 0.016 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/Z covalent geometry : bond 0.00314 / 0.14 ( 8264) covalent geometry : angle 0.57997 / 0.29 (11290) hydrogen bonds : bond 0.04096 / 2.64 ( 546) hydrogen bonds : angle 3.84822 / 2.76 ( 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: 16 poor density : 138 time to evaluate : 0.311 Fit side-chains REVERT: A 6 TYR cc_start: 0.6426 (m-80) cc_final: 0.6206 (m-10) REVERT: A 157 GLN cc_start: 0.7874 (tt0) cc_final: 0.7654 (tt0) REVERT: A 345 TYR cc_start: 0.5467 (m-80) cc_final: 0.5248 (m-80) REVERT: A 450 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.7048 (mm-30) REVERT: A 573 ILE cc_start: 0.8787 (mm) cc_final: 0.8436 (mm) REVERT: A 578 ASP cc_start: 0.7166 (t0) cc_final: 0.6820 (t70) REVERT: B 234 HIS cc_start: 0.7290 (t-90) cc_final: 0.7033 (t70) REVERT: B 268 TYR cc_start: 0.7951 (t80) cc_final: 0.7702 (t80) REVERT: B 450 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.6709 (mp0) REVERT: B 573 ILE cc_start: 0.8776 (mm) cc_final: 0.8426 (mm) outliers start: 16 outliers final: 9 residues processed: 149 average time/residue: 0.0680 time to fit residues: 15.2106 Evaluate side-chains 144 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 133 time to evaluate : 0.315 ------------------------------------------------------------------------------- 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 569 ILE Chi-restraints excluded: chain B residue 28 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 36 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 90 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 234 HIS B 157 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.142630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.117038 restraints weight = 13020.052| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.20 r_work: 0.3332 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.1655 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= 0.152 Angle : 0.589 6.803 11290 Z= 0.296 Chirality : 0.040 0.220 1350 Planarity : 0.005 0.049 1342 Dihedral : 4.344 28.729 1064 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.36 % Allowed : 12.61 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.27), residues: 1012 helix: 2.31 (0.19), residues: 740 sheet: None (None), residues: 0 loop : -1.50 (0.39), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 237 TYR 0.010 0.001 TYR B 6 PHE 0.016 0.001 PHE A 287 TRP 0.011 0.001 TRP B 585 HIS 0.003 0.001 HIS A 544 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 ( 8264) covalent geometry : angle 0.58865 / 0.30 (11290) hydrogen bonds : bond 0.04241 / 2.75 ( 546) hydrogen bonds : angle 3.85438 / 2.77 ( 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 147 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 135 time to evaluate : 0.181 Fit side-chains revert: symmetry clash REVERT: A 6 TYR cc_start: 0.6479 (m-80) cc_final: 0.6236 (m-10) REVERT: A 345 TYR cc_start: 0.5793 (m-80) cc_final: 0.5589 (m-80) REVERT: A 450 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.7203 (mm-30) REVERT: A 573 ILE cc_start: 0.8832 (mm) cc_final: 0.8479 (mm) REVERT: A 578 ASP cc_start: 0.7450 (t0) cc_final: 0.6999 (t70) REVERT: B 234 HIS cc_start: 0.7507 (t-90) cc_final: 0.7217 (t70) REVERT: B 268 TYR cc_start: 0.8058 (t80) cc_final: 0.7798 (t80) REVERT: B 450 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.6929 (mp0) REVERT: B 529 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7976 (mt) REVERT: B 573 ILE cc_start: 0.8819 (mm) cc_final: 0.8467 (mm) REVERT: B 578 ASP cc_start: 0.7398 (t0) cc_final: 0.6986 (t70) outliers start: 12 outliers final: 7 residues processed: 144 average time/residue: 0.0535 time to fit residues: 11.5115 Evaluate side-chains 143 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 133 time to evaluate : 0.288 ------------------------------------------------------------------------------- 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 569 ILE Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 529 LEU 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: 0.1980 chunk 67 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 76 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 101 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 234 HIS A 544 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 = 0.3795 r_free = 0.3795 target = 0.143763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.118294 restraints weight = 12948.722| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.19 r_work: 0.3347 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1708 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= 0.136 Angle : 0.593 11.199 11290 Z= 0.295 Chirality : 0.040 0.128 1350 Planarity : 0.005 0.049 1342 Dihedral : 4.299 28.410 1064 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.70 % Allowed : 12.84 % 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 are not related in a simple way. whole: 1.97 (0.27), residues: 1012 helix: 2.28 (0.19), residues: 744 sheet: None (None), residues: 0 loop : -1.65 (0.39), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 237 TYR 0.010 0.001 TYR B 6 PHE 0.015 0.001 PHE A 287 TRP 0.015 0.001 TRP A 585 HIS 0.005 0.001 HIS A 544 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 ( 8264) covalent geometry : angle 0.59328 / 0.29 (11290) hydrogen bonds : bond 0.04098 / 2.65 ( 546) hydrogen bonds : angle 3.79906 / 2.73 ( 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 153 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 138 time to evaluate : 0.291 Fit side-chains revert: symmetry clash REVERT: A 6 TYR cc_start: 0.6398 (m-80) cc_final: 0.6171 (m-10) REVERT: A 450 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.7204 (mm-30) REVERT: A 486 GLU cc_start: 0.6599 (OUTLIER) cc_final: 0.5242 (mp0) REVERT: A 573 ILE cc_start: 0.8812 (mm) cc_final: 0.8470 (mm) REVERT: A 578 ASP cc_start: 0.7513 (t0) cc_final: 0.7058 (t70) REVERT: B 234 HIS cc_start: 0.7481 (t-90) cc_final: 0.7213 (t70) REVERT: B 268 TYR cc_start: 0.8058 (t80) cc_final: 0.7789 (t80) REVERT: B 347 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8183 (mt-10) REVERT: B 450 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.6859 (mp0) REVERT: B 529 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8000 (mt) REVERT: B 573 ILE cc_start: 0.8797 (mm) cc_final: 0.8454 (mm) REVERT: B 578 ASP cc_start: 0.7512 (t0) cc_final: 0.7070 (t70) outliers start: 15 outliers final: 8 residues processed: 150 average time/residue: 0.0592 time to fit residues: 13.2378 Evaluate side-chains 148 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 136 time to evaluate : 0.201 ------------------------------------------------------------------------------- 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 486 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 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: 2.9990 chunk 65 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 24 optimal weight: 0.0010 chunk 73 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.144598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.119255 restraints weight = 12943.040| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.19 r_work: 0.3362 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1780 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 : 0.591 10.486 11290 Z= 0.293 Chirality : 0.040 0.250 1350 Planarity : 0.005 0.049 1342 Dihedral : 4.246 28.116 1064 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.27), residues: 1012 helix: 2.30 (0.19), residues: 744 sheet: None (None), residues: 0 loop : -1.64 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 237 TYR 0.012 0.001 TYR B 6 PHE 0.013 0.001 PHE A 287 TRP 0.010 0.001 TRP B 424 HIS 0.006 0.001 HIS B 544 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 8264) covalent geometry : angle 0.59073 / 0.29 (11290) hydrogen bonds : bond 0.03950 / 2.56 ( 546) hydrogen bonds : angle 3.77609 / 2.72 ( 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: 16 poor density : 144 time to evaluate : 0.289 Fit side-chains revert: symmetry clash REVERT: A 297 LEU cc_start: 0.8881 (mm) cc_final: 0.8664 (mm) REVERT: A 450 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.7034 (mm-30) REVERT: A 486 GLU cc_start: 0.6419 (OUTLIER) cc_final: 0.5099 (mp0) REVERT: A 573 ILE cc_start: 0.8752 (mm) cc_final: 0.8399 (mm) REVERT: A 578 ASP cc_start: 0.7374 (t0) cc_final: 0.6889 (t70) REVERT: B 268 TYR cc_start: 0.7951 (t80) cc_final: 0.7539 (t80) REVERT: B 450 GLU cc_start: 0.7293 (OUTLIER) cc_final: 0.6917 (mm-30) REVERT: B 529 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8034 (mt) REVERT: B 573 ILE cc_start: 0.8743 (mm) cc_final: 0.8400 (mm) REVERT: B 578 ASP cc_start: 0.7401 (t0) cc_final: 0.6988 (t70) outliers start: 16 outliers final: 10 residues processed: 156 average time/residue: 0.0550 time to fit residues: 12.9317 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 : 0.282 ------------------------------------------------------------------------------- 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 332 VAL Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain A residue 486 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 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: 0.9980 chunk 36 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 38 optimal weight: 0.0980 chunk 87 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 78 optimal weight: 0.0060 chunk 75 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 157 GLN A 234 HIS B 157 GLN B 234 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.145308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.119841 restraints weight = 12901.099| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.20 r_work: 0.3373 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8264 Z= 0.127 Angle : 0.612 15.081 11290 Z= 0.301 Chirality : 0.040 0.279 1350 Planarity : 0.005 0.049 1342 Dihedral : 4.221 27.867 1064 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.93 % Allowed : 12.84 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.27), residues: 1012 helix: 2.28 (0.19), residues: 744 sheet: None (None), residues: 0 loop : -1.57 (0.39), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 237 TYR 0.020 0.001 TYR A 6 PHE 0.013 0.001 PHE A 287 TRP 0.010 0.001 TRP B 424 HIS 0.003 0.001 HIS B 544 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 ( 8264) covalent geometry : angle 0.61249 / 0.30 (11290) hydrogen bonds : bond 0.03885 / 2.50 ( 546) hydrogen bonds : angle 3.78352 / 2.72 ( 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 160 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 143 time to evaluate : 0.190 Fit side-chains revert: symmetry clash REVERT: A 297 LEU cc_start: 0.8885 (mm) cc_final: 0.8666 (mm) REVERT: A 347 GLU cc_start: 0.8402 (mt-10) cc_final: 0.7998 (mt-10) REVERT: A 450 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.7029 (mm-30) REVERT: A 486 GLU cc_start: 0.6446 (OUTLIER) cc_final: 0.5192 (mp0) REVERT: A 573 ILE cc_start: 0.8743 (mm) cc_final: 0.8402 (mm) REVERT: A 578 ASP cc_start: 0.7393 (t0) cc_final: 0.6890 (t70) REVERT: B 243 CYS cc_start: 0.8400 (p) cc_final: 0.8130 (p) REVERT: B 268 TYR cc_start: 0.7949 (t80) cc_final: 0.7674 (t80) REVERT: B 347 GLU cc_start: 0.8398 (mt-10) cc_final: 0.8004 (mt-10) REVERT: B 450 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.6733 (mp0) REVERT: B 529 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8068 (mt) REVERT: B 573 ILE cc_start: 0.8728 (mm) cc_final: 0.8365 (mm) REVERT: B 578 ASP cc_start: 0.7336 (t0) cc_final: 0.6862 (t70) outliers start: 17 outliers final: 11 residues processed: 156 average time/residue: 0.0554 time to fit residues: 12.9139 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 : 0.241 ------------------------------------------------------------------------------- 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 332 VAL Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain A residue 486 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 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 16 optimal weight: 0.9990 chunk 85 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 83 optimal weight: 0.2980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 157 GLN A 234 HIS B 157 GLN B 234 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.144693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.119126 restraints weight = 12993.889| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.21 r_work: 0.3362 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8264 Z= 0.137 Angle : 0.624 15.419 11290 Z= 0.307 Chirality : 0.041 0.274 1350 Planarity : 0.005 0.048 1342 Dihedral : 4.251 27.947 1064 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.70 % Allowed : 13.75 % Favored : 84.55 % 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 are not related in a simple way. whole: 1.95 (0.27), residues: 1012 helix: 2.23 (0.19), residues: 744 sheet: None (None), residues: 0 loop : -1.53 (0.39), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 237 TYR 0.022 0.001 TYR A 6 PHE 0.013 0.001 PHE B 287 TRP 0.009 0.001 TRP B 424 HIS 0.003 0.001 HIS B 544 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 8264) covalent geometry : angle 0.62352 / 0.31 (11290) hydrogen bonds : bond 0.04003 / 2.59 ( 546) hydrogen bonds : angle 3.81588 / 2.74 ( 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 150 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 135 time to evaluate : 0.284 Fit side-chains revert: symmetry clash REVERT: A 297 LEU cc_start: 0.8903 (mm) cc_final: 0.8681 (mm) REVERT: A 450 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.7049 (mm-30) REVERT: A 486 GLU cc_start: 0.6459 (OUTLIER) cc_final: 0.5227 (mp0) REVERT: A 573 ILE cc_start: 0.8710 (mm) cc_final: 0.8358 (mm) REVERT: A 578 ASP cc_start: 0.7439 (t0) cc_final: 0.6932 (t0) REVERT: B 243 CYS cc_start: 0.8502 (p) cc_final: 0.8202 (p) REVERT: B 268 TYR cc_start: 0.7966 (t80) cc_final: 0.7675 (t80) REVERT: B 450 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.6739 (mp0) REVERT: B 529 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8081 (mt) REVERT: B 573 ILE cc_start: 0.8703 (mm) cc_final: 0.8356 (mm) REVERT: B 578 ASP cc_start: 0.7438 (t0) cc_final: 0.6868 (t70) outliers start: 15 outliers final: 11 residues processed: 147 average time/residue: 0.0536 time to fit residues: 11.8634 Evaluate side-chains 147 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 0.205 ------------------------------------------------------------------------------- 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 332 VAL Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain A residue 486 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 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 73 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 78 optimal weight: 0.0570 chunk 20 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 97 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 234 HIS B 234 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.145109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.119681 restraints weight = 12776.277| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.19 r_work: 0.3369 rms_B_bonded: 3.00 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: 0.8528 moved from start: 0.1970 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= 0.132 Angle : 0.623 15.763 11290 Z= 0.306 Chirality : 0.040 0.276 1350 Planarity : 0.005 0.048 1342 Dihedral : 4.225 27.974 1064 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.70 % Allowed : 13.64 % 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 are not related in a simple way. whole: 1.94 (0.27), residues: 1012 helix: 2.23 (0.19), residues: 744 sheet: None (None), residues: 0 loop : -1.55 (0.39), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 237 TYR 0.024 0.001 TYR A 6 PHE 0.012 0.001 PHE A 287 TRP 0.010 0.001 TRP B 424 HIS 0.003 0.001 HIS B 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 8264) covalent geometry : angle 0.62304 / 0.31 (11290) hydrogen bonds : bond 0.03924 / 2.54 ( 546) hydrogen bonds : angle 3.81744 / 2.75 ( 1626) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1676.60 seconds wall clock time: 29 minutes 32.86 seconds (1772.86 seconds total)