Starting phenix.real_space_refine on Wed Sep 17 13:09:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ri1_19180/09_2025/8ri1_19180.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ri1_19180/09_2025/8ri1_19180.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ri1_19180/09_2025/8ri1_19180.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ri1_19180/09_2025/8ri1_19180.map" model { file = "/net/cci-nas-00/data/ceres_data/8ri1_19180/09_2025/8ri1_19180.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ri1_19180/09_2025/8ri1_19180.cif" } resolution = 3.6 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= 0.002 sd= 0.037 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 34 5.16 5 C 5652 2.51 5 N 1472 2.21 5 O 1668 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8834 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4385 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 17, 'TRANS': 552} Chain: "B" Number of atoms: 4385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4385 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 17, 'TRANS': 552} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.45, per 1000 atoms: 0.28 Number of scatterers: 8834 At special positions: 0 Unit cell: (74.425, 87.02, 133.965, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 34 16.00 P 6 15.00 Mg 2 11.99 O 1668 8.00 N 1472 7.00 C 5652 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.11 Conformation dependent library (CDL) restraints added in 348.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2096 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 4 sheets defined 71.0% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 11 through 22 removed outlier: 3.633A pdb=" N THR A 22 " --> pdb=" O LEU A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 61 Proline residue: A 47 - end of helix removed outlier: 4.307A pdb=" N LYS A 51 " --> pdb=" O PRO A 47 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASN A 61 " --> pdb=" O PHE A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 108 Processing helix chain 'A' and resid 111 through 118 removed outlier: 3.840A pdb=" N PHE A 115 " --> pdb=" O PRO A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 163 removed outlier: 3.520A pdb=" N THR A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N THR A 139 " --> pdb=" O LYS A 135 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N THR A 140 " --> pdb=" O GLU A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 210 Proline residue: A 175 - end of helix removed outlier: 3.555A pdb=" N VAL A 182 " --> pdb=" O ALA A 178 " (cutoff:3.500A) Proline residue: A 183 - end of helix Processing helix chain 'A' and resid 212 through 220 Processing helix chain 'A' and resid 221 through 272 Proline residue: A 252 - end of helix removed outlier: 4.268A pdb=" N SER A 255 " --> pdb=" O GLY A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 314 removed outlier: 3.573A pdb=" N ILE A 294 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N MET A 295 " --> pdb=" O PHE A 291 " (cutoff:3.500A) Proline residue: A 296 - end of helix removed outlier: 4.115A pdb=" N GLN A 299 " --> pdb=" O MET A 295 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N THR A 302 " --> pdb=" O GLY A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 321 Processing helix chain 'A' and resid 379 through 388 removed outlier: 3.513A pdb=" N LEU A 383 " --> pdb=" O GLY A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 408 Processing helix chain 'A' and resid 409 through 416 removed outlier: 3.516A pdb=" N HIS A 416 " --> pdb=" O SER A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 438 removed outlier: 3.628A pdb=" N ASN A 434 " --> pdb=" O THR A 430 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE A 435 " --> pdb=" O ILE A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 454 Processing helix chain 'A' and resid 457 through 464 Processing helix chain 'A' and resid 473 through 477 Processing helix chain 'A' and resid 482 through 495 removed outlier: 3.623A pdb=" N ARG A 495 " --> pdb=" O ARG A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 528 Processing helix chain 'A' and resid 536 through 540 removed outlier: 3.553A pdb=" N THR A 539 " --> pdb=" O ARG A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 567 Processing helix chain 'A' and resid 568 through 570 No H-bonds generated for 'chain 'A' and resid 568 through 570' Processing helix chain 'A' and resid 571 through 578 Processing helix chain 'B' and resid 11 through 22 Processing helix chain 'B' and resid 25 through 49 Proline residue: B 47 - end of helix Processing helix chain 'B' and resid 49 through 63 Processing helix chain 'B' and resid 66 through 109 Processing helix chain 'B' and resid 111 through 118 removed outlier: 3.821A pdb=" N PHE B 115 " --> pdb=" O PRO B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 163 removed outlier: 3.502A pdb=" N THR B 139 " --> pdb=" O LYS B 135 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N THR B 140 " --> pdb=" O GLU B 136 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N HIS B 141 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ILE B 142 " --> pdb=" O ILE B 138 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N SER B 143 " --> pdb=" O THR B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 210 removed outlier: 3.661A pdb=" N VAL B 170 " --> pdb=" O LEU B 166 " (cutoff:3.500A) Proline residue: B 175 - end of helix Proline residue: B 183 - end of helix removed outlier: 3.993A pdb=" N ALA B 200 " --> pdb=" O GLN B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 219 Processing helix chain 'B' and resid 221 through 273 removed outlier: 4.089A pdb=" N GLY B 251 " --> pdb=" O GLN B 247 " (cutoff:3.500A) Proline residue: B 252 - end of helix removed outlier: 3.816A pdb=" N MET B 271 " --> pdb=" O GLY B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 321 removed outlier: 3.738A pdb=" N MET B 295 " --> pdb=" O PHE B 291 " (cutoff:3.500A) Proline residue: B 296 - end of helix removed outlier: 3.700A pdb=" N GLN B 299 " --> pdb=" O MET B 295 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE B 311 " --> pdb=" O LEU B 307 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG B 316 " --> pdb=" O GLY B 312 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N MET B 317 " --> pdb=" O ALA B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 388 Processing helix chain 'B' and resid 404 through 408 Processing helix chain 'B' and resid 409 through 414 Processing helix chain 'B' and resid 430 through 437 Processing helix chain 'B' and resid 445 through 455 Processing helix chain 'B' and resid 457 through 462 Processing helix chain 'B' and resid 480 through 496 removed outlier: 3.633A pdb=" N ASN B 496 " --> pdb=" O ALA B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 526 Processing helix chain 'B' and resid 559 through 568 removed outlier: 3.847A pdb=" N GLY B 568 " --> pdb=" O MET B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 578 removed outlier: 3.720A pdb=" N ASP B 572 " --> pdb=" O GLY B 568 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 360 through 364 removed outlier: 6.252A pdb=" N VAL A 360 " --> pdb=" O ARG A 345 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ARG A 345 " --> pdb=" O VAL A 360 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 417 through 420 removed outlier: 6.272A pdb=" N THR A 370 " --> pdb=" O VAL A 532 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N LEU A 547 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ALA A 371 " --> pdb=" O LEU A 547 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL A 549 " --> pdb=" O ALA A 371 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N VAL A 373 " --> pdb=" O VAL A 549 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N PHE A 548 " --> pdb=" O THR A 555 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 357 through 364 removed outlier: 6.869A pdb=" N LYS B 358 " --> pdb=" O SER B 347 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N SER B 347 " --> pdb=" O LYS B 358 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N VAL B 360 " --> pdb=" O ARG B 345 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG B 345 " --> pdb=" O VAL B 360 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 417 through 420 removed outlier: 6.004A pdb=" N GLY B 418 " --> pdb=" O MET B 501 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N ASP B 503 " --> pdb=" O GLY B 418 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N VAL B 420 " --> pdb=" O ASP B 503 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LEU B 500 " --> pdb=" O ILE B 531 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N ILE B 533 " --> pdb=" O LEU B 500 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N LEU B 502 " --> pdb=" O ILE B 533 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLN B 545 " --> pdb=" O VAL B 369 " (cutoff:3.500A) 601 hydrogen bonds defined for protein. 1773 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: 1.40 Time building geometry restraints manager: 1.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.91: 1 0.91 - 1.16: 0 1.16 - 1.42: 3540 1.42 - 1.67: 5362 1.67 - 1.92: 67 Bond restraints: 8970 Sorted by residual: bond pdb=" CG PRO A 252 " pdb=" CD PRO A 252 " ideal model delta sigma weight residual 1.503 0.658 0.845 3.40e-02 8.65e+02 6.18e+02 bond pdb=" N PRO A 252 " pdb=" CA PRO A 252 " ideal model delta sigma weight residual 1.468 1.285 0.183 1.10e-02 8.26e+03 2.77e+02 bond pdb=" C GLY A 251 " pdb=" N PRO A 252 " ideal model delta sigma weight residual 1.332 1.468 -0.135 8.90e-03 1.26e+04 2.31e+02 bond pdb=" C GLY A 251 " pdb=" O GLY A 251 " ideal model delta sigma weight residual 1.235 1.411 -0.176 1.35e-02 5.49e+03 1.69e+02 bond pdb=" CA PRO A 252 " pdb=" CB PRO A 252 " ideal model delta sigma weight residual 1.536 1.341 0.195 1.69e-02 3.50e+03 1.33e+02 ... (remaining 8965 not shown) Histogram of bond angle deviations from ideal: 0.00 - 21.19: 12144 21.19 - 42.39: 11 42.39 - 63.58: 0 63.58 - 84.78: 0 84.78 - 105.97: 1 Bond angle restraints: 12156 Sorted by residual: angle pdb=" CB PRO A 252 " pdb=" CG PRO A 252 " pdb=" CD PRO A 252 " ideal model delta sigma weight residual 106.10 0.13 105.97 3.20e+00 9.77e-02 1.10e+03 angle pdb=" CA PRO A 252 " pdb=" N PRO A 252 " pdb=" CD PRO A 252 " ideal model delta sigma weight residual 112.00 82.49 29.51 1.40e+00 5.10e-01 4.44e+02 angle pdb=" C THR B 328 " pdb=" CA THR B 328 " pdb=" CB THR B 328 " ideal model delta sigma weight residual 111.22 85.37 25.85 1.23e+00 6.61e-01 4.42e+02 angle pdb=" N ALA B 119 " pdb=" CA ALA B 119 " pdb=" CB ALA B 119 " ideal model delta sigma weight residual 110.45 81.22 29.23 1.44e+00 4.82e-01 4.12e+02 angle pdb=" N ASN B 118 " pdb=" CA ASN B 118 " pdb=" C ASN B 118 " ideal model delta sigma weight residual 109.24 82.23 27.01 1.67e+00 3.59e-01 2.62e+02 ... (remaining 12151 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.12: 4751 19.12 - 38.25: 555 38.25 - 57.37: 124 57.37 - 76.49: 13 76.49 - 95.62: 11 Dihedral angle restraints: 5454 sinusoidal: 2190 harmonic: 3264 Sorted by residual: dihedral pdb=" N ALA B 119 " pdb=" C ALA B 119 " pdb=" CA ALA B 119 " pdb=" CB ALA B 119 " ideal model delta harmonic sigma weight residual 122.90 88.84 34.06 0 2.50e+00 1.60e-01 1.86e+02 dihedral pdb=" N ALA A 280 " pdb=" C ALA A 280 " pdb=" CA ALA A 280 " pdb=" CB ALA A 280 " ideal model delta harmonic sigma weight residual 122.90 93.56 29.34 0 2.50e+00 1.60e-01 1.38e+02 dihedral pdb=" C THR B 328 " pdb=" N THR B 328 " pdb=" CA THR B 328 " pdb=" CB THR B 328 " ideal model delta harmonic sigma weight residual -122.00 -94.07 -27.93 0 2.50e+00 1.60e-01 1.25e+02 ... (remaining 5451 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.217: 1454 0.217 - 0.434: 4 0.434 - 0.652: 7 0.652 - 0.869: 2 0.869 - 1.086: 1 Chirality restraints: 1468 Sorted by residual: chirality pdb=" CA ASP A 344 " pdb=" N ASP A 344 " pdb=" C ASP A 344 " pdb=" CB ASP A 344 " both_signs ideal model delta sigma weight residual False 2.51 1.42 1.09 2.00e-01 2.50e+01 2.95e+01 chirality pdb=" CA THR A 444 " pdb=" N THR A 444 " pdb=" C THR A 444 " pdb=" CB THR A 444 " both_signs ideal model delta sigma weight residual False 2.53 1.77 0.76 2.00e-01 2.50e+01 1.43e+01 chirality pdb=" CA ASN B 466 " pdb=" N ASN B 466 " pdb=" C ASN B 466 " pdb=" CB ASN B 466 " both_signs ideal model delta sigma weight residual False 2.51 1.77 0.74 2.00e-01 2.50e+01 1.37e+01 ... (remaining 1465 not shown) Planarity restraints: 1514 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 212 " -0.018 2.00e-02 2.50e+03 3.68e-02 1.36e+01 pdb=" C GLU B 212 " 0.064 2.00e-02 2.50e+03 pdb=" O GLU B 212 " -0.024 2.00e-02 2.50e+03 pdb=" N ILE B 213 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 174 " -0.064 5.00e-02 4.00e+02 9.18e-02 1.35e+01 pdb=" N PRO A 175 " 0.158 5.00e-02 4.00e+02 pdb=" CA PRO A 175 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 175 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 252 " -0.017 2.00e-02 2.50e+03 3.34e-02 1.12e+01 pdb=" C PRO A 252 " 0.058 2.00e-02 2.50e+03 pdb=" O PRO A 252 " -0.021 2.00e-02 2.50e+03 pdb=" N LEU A 253 " -0.020 2.00e-02 2.50e+03 ... (remaining 1511 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.41: 56 2.41 - 3.03: 6496 3.03 - 3.65: 13499 3.65 - 4.28: 19036 4.28 - 4.90: 31614 Nonbonded interactions: 70701 Sorted by model distance: nonbonded pdb=" O THR B 328 " pdb=" OG1 THR B 328 " model vdw 1.783 3.040 nonbonded pdb=" O2B ATP B 601 " pdb="MG MG B 602 " model vdw 1.791 2.170 nonbonded pdb=" O2G ATP A 601 " pdb="MG MG A 602 " model vdw 1.826 2.170 nonbonded pdb=" O2B ATP A 601 " pdb="MG MG A 602 " model vdw 1.838 2.170 nonbonded pdb=" O2G ATP B 601 " pdb="MG MG B 602 " model vdw 1.859 2.170 ... (remaining 70696 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 group one per residue 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: 0.710 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: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.520 Find NCS groups from input model: 0.140 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 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 : 0.012 0.845 8970 Z= 0.462 Angle : 1.562 105.971 12156 Z= 0.788 Chirality : 0.066 1.086 1468 Planarity : 0.005 0.092 1514 Dihedral : 16.829 95.616 3358 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 42.39 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.34 % Favored : 93.40 % Rotamer: Outliers : 0.42 % Allowed : 24.27 % Favored : 75.31 % Cbeta Deviations : 1.43 % 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: 1.35 (0.27), residues: 1136 helix: 2.40 (0.20), residues: 734 sheet: -3.17 (0.68), residues: 38 loop : -1.98 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 345 TYR 0.007 0.001 TYR A 83 PHE 0.013 0.001 PHE A 75 TRP 0.005 0.001 TRP B 104 HIS 0.004 0.000 HIS A 141 Details of bonding type rmsd covalent geometry : bond 0.01151 ( 8970) covalent geometry : angle 1.56245 (12156) hydrogen bonds : bond 0.13877 ( 601) hydrogen bonds : angle 5.77199 ( 1773) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 155 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 158 average time/residue: 0.0879 time to fit residues: 20.2602 Evaluate side-chains 152 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 150 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain B residue 255 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 8.9990 chunk 113 optimal weight: 9.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 4.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN A 272 GLN B 577 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.154827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.119861 restraints weight = 14856.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.124186 restraints weight = 7470.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.126921 restraints weight = 4977.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.128465 restraints weight = 3936.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.129182 restraints weight = 3470.222| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 8970 Z= 0.242 Angle : 0.744 13.712 12156 Z= 0.384 Chirality : 0.046 0.206 1468 Planarity : 0.006 0.118 1514 Dihedral : 8.949 88.151 1291 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.34 % Favored : 93.57 % Rotamer: Outliers : 4.48 % Allowed : 23.02 % Favored : 72.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 1.02 (0.26), residues: 1136 helix: 2.06 (0.19), residues: 764 sheet: -2.95 (0.50), residues: 58 loop : -2.19 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 345 TYR 0.011 0.001 TYR B 419 PHE 0.024 0.002 PHE B 286 TRP 0.009 0.002 TRP A 413 HIS 0.008 0.001 HIS A 141 Details of bonding type rmsd covalent geometry : bond 0.00556 ( 8970) covalent geometry : angle 0.74378 (12156) hydrogen bonds : bond 0.05789 ( 601) hydrogen bonds : angle 4.73896 ( 1773) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 151 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 188 MET cc_start: 0.7752 (tpp) cc_final: 0.7410 (tpp) REVERT: A 271 MET cc_start: 0.7326 (tmm) cc_final: 0.7123 (tmm) REVERT: A 317 MET cc_start: 0.8769 (OUTLIER) cc_final: 0.7974 (mtm) REVERT: A 372 ILE cc_start: 0.8930 (OUTLIER) cc_final: 0.8667 (mt) REVERT: A 460 PHE cc_start: 0.7368 (m-80) cc_final: 0.7125 (m-80) REVERT: A 525 MET cc_start: 0.6492 (tpt) cc_final: 0.6137 (tpt) REVERT: A 559 THR cc_start: 0.8444 (OUTLIER) cc_final: 0.8130 (p) REVERT: B 132 MET cc_start: 0.7688 (tpp) cc_final: 0.7413 (tpp) REVERT: B 259 MET cc_start: 0.7567 (tmm) cc_final: 0.7341 (tmm) REVERT: B 372 ILE cc_start: 0.8862 (OUTLIER) cc_final: 0.8632 (mt) REVERT: B 414 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.7601 (mtt-85) REVERT: B 430 THR cc_start: 0.8859 (OUTLIER) cc_final: 0.8332 (t) REVERT: B 433 GLU cc_start: 0.8278 (tm-30) cc_final: 0.7741 (tm-30) outliers start: 43 outliers final: 23 residues processed: 180 average time/residue: 0.0722 time to fit residues: 19.2597 Evaluate side-chains 165 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 136 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 437 TYR Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 414 ARG Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 447 GLU Chi-restraints excluded: chain B residue 559 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 63 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 67 optimal weight: 0.5980 chunk 109 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 chunk 101 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.156643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.121702 restraints weight = 14773.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.126072 restraints weight = 7373.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.128792 restraints weight = 4894.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.130378 restraints weight = 3883.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.131082 restraints weight = 3422.036| |-----------------------------------------------------------------------------| r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8970 Z= 0.165 Angle : 0.633 9.172 12156 Z= 0.328 Chirality : 0.043 0.190 1468 Planarity : 0.005 0.071 1514 Dihedral : 8.955 89.155 1288 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.99 % Favored : 93.93 % Rotamer: Outliers : 5.00 % Allowed : 23.54 % Favored : 71.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 1.11 (0.26), residues: 1136 helix: 2.14 (0.19), residues: 764 sheet: -2.46 (0.46), residues: 80 loop : -2.23 (0.35), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 345 TYR 0.008 0.001 TYR B 391 PHE 0.014 0.002 PHE A 468 TRP 0.006 0.001 TRP A 413 HIS 0.007 0.001 HIS A 141 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 8970) covalent geometry : angle 0.63338 (12156) hydrogen bonds : bond 0.05271 ( 601) hydrogen bonds : angle 4.41681 ( 1773) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 159 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 188 MET cc_start: 0.7798 (tpp) cc_final: 0.7402 (tpp) REVERT: A 214 ARG cc_start: 0.8776 (OUTLIER) cc_final: 0.8092 (mtm-85) REVERT: A 268 TYR cc_start: 0.6051 (t80) cc_final: 0.5272 (t80) REVERT: A 326 GLU cc_start: 0.6226 (pm20) cc_final: 0.5758 (pm20) REVERT: A 460 PHE cc_start: 0.7341 (m-80) cc_final: 0.7040 (m-80) REVERT: A 559 THR cc_start: 0.8401 (OUTLIER) cc_final: 0.8072 (p) REVERT: B 132 MET cc_start: 0.7599 (tpp) cc_final: 0.7354 (tpp) REVERT: B 259 MET cc_start: 0.7513 (tmm) cc_final: 0.7199 (tmm) REVERT: B 317 MET cc_start: 0.8597 (mtp) cc_final: 0.8374 (mtp) REVERT: B 414 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.8209 (mtt-85) REVERT: B 430 THR cc_start: 0.8790 (OUTLIER) cc_final: 0.8248 (t) REVERT: B 433 GLU cc_start: 0.8325 (tm-30) cc_final: 0.7744 (tm-30) outliers start: 48 outliers final: 26 residues processed: 193 average time/residue: 0.0873 time to fit residues: 24.4777 Evaluate side-chains 174 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 144 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 437 TYR Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 286 PHE Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 414 ARG Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 559 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 42 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 25 optimal weight: 9.9990 chunk 10 optimal weight: 0.5980 chunk 111 optimal weight: 0.0070 chunk 22 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 20 optimal weight: 0.0870 chunk 70 optimal weight: 0.1980 chunk 77 optimal weight: 0.3980 chunk 86 optimal weight: 4.9990 overall best weight: 0.2576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 GLN A 485 GLN B 434 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.162001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.127252 restraints weight = 14770.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.131873 restraints weight = 7254.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.134747 restraints weight = 4767.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.136417 restraints weight = 3753.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.137175 restraints weight = 3292.981| |-----------------------------------------------------------------------------| r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8970 Z= 0.129 Angle : 0.604 9.431 12156 Z= 0.309 Chirality : 0.041 0.192 1468 Planarity : 0.005 0.060 1514 Dihedral : 8.419 84.941 1288 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.55 % Favored : 94.37 % Rotamer: Outliers : 4.38 % Allowed : 23.85 % Favored : 71.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 1.26 (0.26), residues: 1136 helix: 2.20 (0.19), residues: 766 sheet: -1.86 (0.56), residues: 54 loop : -2.26 (0.33), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 345 TYR 0.007 0.001 TYR A 268 PHE 0.021 0.002 PHE A 75 TRP 0.005 0.001 TRP A 413 HIS 0.008 0.001 HIS A 141 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 8970) covalent geometry : angle 0.60371 (12156) hydrogen bonds : bond 0.04465 ( 601) hydrogen bonds : angle 4.15057 ( 1773) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 163 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: A 188 MET cc_start: 0.7694 (tpp) cc_final: 0.7347 (tpp) REVERT: A 214 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.8095 (mtm-85) REVERT: A 317 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.7647 (mtm) REVERT: A 342 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.7811 (tt0) REVERT: A 460 PHE cc_start: 0.7292 (m-80) cc_final: 0.7025 (m-80) REVERT: A 525 MET cc_start: 0.6435 (tpt) cc_final: 0.6133 (tpt) REVERT: A 559 THR cc_start: 0.8314 (OUTLIER) cc_final: 0.7981 (p) REVERT: B 132 MET cc_start: 0.7469 (tpp) cc_final: 0.7200 (tpp) REVERT: B 243 GLU cc_start: 0.8227 (tm-30) cc_final: 0.7739 (tm-30) REVERT: B 259 MET cc_start: 0.7565 (tmm) cc_final: 0.7176 (tmm) REVERT: B 317 MET cc_start: 0.8484 (mtp) cc_final: 0.8222 (mtp) REVERT: B 372 ILE cc_start: 0.8653 (OUTLIER) cc_final: 0.8444 (mt) REVERT: B 414 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.8092 (mtt-85) REVERT: B 430 THR cc_start: 0.8705 (p) cc_final: 0.8219 (t) REVERT: B 433 GLU cc_start: 0.8303 (tm-30) cc_final: 0.7803 (tm-30) outliers start: 42 outliers final: 21 residues processed: 191 average time/residue: 0.0895 time to fit residues: 24.3406 Evaluate side-chains 177 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 150 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 437 TYR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 286 PHE Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 414 ARG Chi-restraints excluded: chain B residue 559 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 1 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 35 optimal weight: 0.0770 chunk 66 optimal weight: 0.6980 chunk 98 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN B 434 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.160573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.125711 restraints weight = 14710.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.130156 restraints weight = 7263.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.132894 restraints weight = 4808.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.134596 restraints weight = 3808.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.135495 restraints weight = 3333.488| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8970 Z= 0.132 Angle : 0.585 9.137 12156 Z= 0.301 Chirality : 0.041 0.235 1468 Planarity : 0.004 0.058 1514 Dihedral : 8.432 84.946 1288 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.55 % Favored : 94.37 % Rotamer: Outliers : 4.69 % Allowed : 25.10 % Favored : 70.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 1.25 (0.26), residues: 1136 helix: 2.20 (0.19), residues: 766 sheet: -1.85 (0.56), residues: 54 loop : -2.27 (0.33), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 345 TYR 0.008 0.001 TYR B 391 PHE 0.019 0.002 PHE A 384 TRP 0.006 0.001 TRP B 104 HIS 0.009 0.001 HIS A 141 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 8970) covalent geometry : angle 0.58538 (12156) hydrogen bonds : bond 0.04485 ( 601) hydrogen bonds : angle 4.08767 ( 1773) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 158 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 188 MET cc_start: 0.7743 (tpp) cc_final: 0.7391 (tpp) REVERT: A 214 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.8127 (mtm-85) REVERT: A 268 TYR cc_start: 0.5751 (t80) cc_final: 0.5093 (t80) REVERT: A 272 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.8386 (mm-40) REVERT: A 286 PHE cc_start: 0.7483 (t80) cc_final: 0.7214 (t80) REVERT: A 317 MET cc_start: 0.8350 (OUTLIER) cc_final: 0.7573 (mtm) REVERT: A 342 GLN cc_start: 0.8371 (OUTLIER) cc_final: 0.7801 (tt0) REVERT: A 460 PHE cc_start: 0.7281 (m-80) cc_final: 0.6999 (m-80) REVERT: A 559 THR cc_start: 0.8299 (OUTLIER) cc_final: 0.7982 (p) REVERT: B 132 MET cc_start: 0.7492 (tpp) cc_final: 0.7251 (tpp) REVERT: B 243 GLU cc_start: 0.8247 (tm-30) cc_final: 0.7783 (tm-30) REVERT: B 259 MET cc_start: 0.7590 (tmm) cc_final: 0.7165 (tmm) REVERT: B 271 MET cc_start: 0.7674 (mtp) cc_final: 0.7320 (ttm) REVERT: B 286 PHE cc_start: 0.8334 (OUTLIER) cc_final: 0.7781 (m-80) REVERT: B 317 MET cc_start: 0.8503 (mtp) cc_final: 0.8257 (mtp) REVERT: B 372 ILE cc_start: 0.8629 (OUTLIER) cc_final: 0.8402 (mt) REVERT: B 423 GLU cc_start: 0.7809 (pm20) cc_final: 0.7489 (pm20) REVERT: B 430 THR cc_start: 0.8669 (p) cc_final: 0.8224 (t) REVERT: B 478 MET cc_start: 0.8819 (tpp) cc_final: 0.8612 (mmt) outliers start: 45 outliers final: 26 residues processed: 188 average time/residue: 0.0839 time to fit residues: 22.8560 Evaluate side-chains 179 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 146 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 272 GLN Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 437 TYR Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 286 PHE Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 559 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 71 optimal weight: 0.9980 chunk 108 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 77 optimal weight: 0.0980 chunk 48 optimal weight: 0.2980 chunk 24 optimal weight: 0.9980 chunk 104 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.161567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.126819 restraints weight = 14725.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.131294 restraints weight = 7268.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.134143 restraints weight = 4803.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.135765 restraints weight = 3789.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.136365 restraints weight = 3323.598| |-----------------------------------------------------------------------------| r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8970 Z= 0.126 Angle : 0.591 9.315 12156 Z= 0.302 Chirality : 0.041 0.213 1468 Planarity : 0.004 0.057 1514 Dihedral : 8.281 82.748 1288 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.37 % Favored : 94.54 % Rotamer: Outliers : 4.90 % Allowed : 24.79 % Favored : 70.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 1.28 (0.26), residues: 1136 helix: 2.18 (0.19), residues: 766 sheet: -1.56 (0.67), residues: 44 loop : -2.20 (0.32), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 201 TYR 0.006 0.001 TYR B 391 PHE 0.016 0.002 PHE B 160 TRP 0.004 0.001 TRP B 104 HIS 0.004 0.001 HIS A 141 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 8970) covalent geometry : angle 0.59052 (12156) hydrogen bonds : bond 0.04388 ( 601) hydrogen bonds : angle 4.01649 ( 1773) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 158 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 MET cc_start: 0.7739 (tpp) cc_final: 0.7388 (tpp) REVERT: A 214 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.8124 (mtm-85) REVERT: A 268 TYR cc_start: 0.5783 (t80) cc_final: 0.5137 (t80) REVERT: A 271 MET cc_start: 0.6975 (tmm) cc_final: 0.6713 (tmm) REVERT: A 317 MET cc_start: 0.8210 (OUTLIER) cc_final: 0.7416 (mtm) REVERT: A 342 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.7785 (tt0) REVERT: A 391 TYR cc_start: 0.9247 (m-80) cc_final: 0.8964 (m-80) REVERT: A 460 PHE cc_start: 0.7294 (m-80) cc_final: 0.7001 (m-80) REVERT: A 525 MET cc_start: 0.6146 (tpt) cc_final: 0.5930 (tpt) REVERT: A 559 THR cc_start: 0.8246 (OUTLIER) cc_final: 0.7953 (p) REVERT: B 132 MET cc_start: 0.7466 (tpp) cc_final: 0.7223 (tpp) REVERT: B 243 GLU cc_start: 0.8235 (tm-30) cc_final: 0.7787 (tm-30) REVERT: B 259 MET cc_start: 0.7628 (tmm) cc_final: 0.7184 (tmm) REVERT: B 271 MET cc_start: 0.7583 (mtp) cc_final: 0.7240 (ttm) REVERT: B 286 PHE cc_start: 0.8282 (OUTLIER) cc_final: 0.7752 (m-80) REVERT: B 317 MET cc_start: 0.8511 (mtp) cc_final: 0.8297 (mtp) REVERT: B 372 ILE cc_start: 0.8548 (OUTLIER) cc_final: 0.8345 (mt) REVERT: B 423 GLU cc_start: 0.7865 (pm20) cc_final: 0.7543 (pm20) REVERT: B 430 THR cc_start: 0.8656 (p) cc_final: 0.8235 (t) REVERT: B 478 MET cc_start: 0.8796 (tpp) cc_final: 0.8595 (mmt) outliers start: 47 outliers final: 29 residues processed: 189 average time/residue: 0.0819 time to fit residues: 22.2853 Evaluate side-chains 180 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 145 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 272 GLN Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 437 TYR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 286 PHE Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 559 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 31 optimal weight: 0.0980 chunk 77 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.0010 chunk 76 optimal weight: 0.6980 overall best weight: 0.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN B 129 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.156788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.120667 restraints weight = 14630.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.125431 restraints weight = 7009.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.128453 restraints weight = 4517.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.129932 restraints weight = 3498.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.131174 restraints weight = 3075.762| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8970 Z= 0.125 Angle : 0.585 9.297 12156 Z= 0.298 Chirality : 0.041 0.241 1468 Planarity : 0.004 0.057 1514 Dihedral : 8.147 80.603 1288 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.28 % Favored : 94.63 % Rotamer: Outliers : 5.10 % Allowed : 25.00 % Favored : 69.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 1.30 (0.26), residues: 1136 helix: 2.14 (0.19), residues: 768 sheet: -1.28 (0.79), residues: 34 loop : -2.12 (0.31), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 345 TYR 0.005 0.001 TYR B 391 PHE 0.015 0.002 PHE B 160 TRP 0.016 0.002 TRP A 104 HIS 0.004 0.001 HIS A 141 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 8970) covalent geometry : angle 0.58536 (12156) hydrogen bonds : bond 0.04283 ( 601) hydrogen bonds : angle 3.97800 ( 1773) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 155 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 141 HIS cc_start: 0.7187 (m-70) cc_final: 0.6948 (m90) REVERT: A 188 MET cc_start: 0.7721 (tpp) cc_final: 0.7387 (tpp) REVERT: A 214 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.8080 (mtm-85) REVERT: A 268 TYR cc_start: 0.5733 (t80) cc_final: 0.5028 (t80) REVERT: A 271 MET cc_start: 0.6953 (tmm) cc_final: 0.6626 (tmm) REVERT: A 272 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.7234 (mp10) REVERT: A 317 MET cc_start: 0.8190 (OUTLIER) cc_final: 0.7392 (mtm) REVERT: A 342 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.7771 (tt0) REVERT: A 391 TYR cc_start: 0.9223 (m-80) cc_final: 0.8942 (m-80) REVERT: A 449 GLU cc_start: 0.8799 (mm-30) cc_final: 0.8493 (mt-10) REVERT: A 460 PHE cc_start: 0.7309 (m-80) cc_final: 0.7008 (m-80) REVERT: A 525 MET cc_start: 0.5829 (tpt) cc_final: 0.5601 (tpt) REVERT: A 559 THR cc_start: 0.8203 (OUTLIER) cc_final: 0.7910 (p) REVERT: B 243 GLU cc_start: 0.8231 (tm-30) cc_final: 0.7785 (tm-30) REVERT: B 259 MET cc_start: 0.7637 (tmm) cc_final: 0.7181 (tmm) REVERT: B 271 MET cc_start: 0.7569 (mtp) cc_final: 0.7204 (ttm) REVERT: B 286 PHE cc_start: 0.8284 (OUTLIER) cc_final: 0.7755 (m-80) REVERT: B 317 MET cc_start: 0.8530 (mtp) cc_final: 0.8317 (mtp) REVERT: B 423 GLU cc_start: 0.8005 (pm20) cc_final: 0.7758 (pm20) REVERT: B 430 THR cc_start: 0.8598 (OUTLIER) cc_final: 0.8169 (t) REVERT: B 478 MET cc_start: 0.8812 (tpp) cc_final: 0.8569 (mmt) REVERT: B 536 ARG cc_start: 0.8264 (ptm160) cc_final: 0.7766 (ptm160) outliers start: 49 outliers final: 30 residues processed: 184 average time/residue: 0.0819 time to fit residues: 21.7420 Evaluate side-chains 185 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 148 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 272 GLN Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 437 TYR Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 286 PHE Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 559 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 10 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 3 optimal weight: 9.9990 chunk 109 optimal weight: 3.9990 chunk 32 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 485 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.157592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.121822 restraints weight = 14830.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.126207 restraints weight = 7490.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.128915 restraints weight = 5021.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.130517 restraints weight = 4007.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.131138 restraints weight = 3534.214| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8970 Z= 0.179 Angle : 0.645 11.712 12156 Z= 0.325 Chirality : 0.043 0.241 1468 Planarity : 0.005 0.058 1514 Dihedral : 8.457 79.694 1288 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.81 % Favored : 94.10 % Rotamer: Outliers : 5.10 % Allowed : 25.31 % Favored : 69.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 1.20 (0.26), residues: 1136 helix: 2.07 (0.19), residues: 764 sheet: -1.33 (0.67), residues: 44 loop : -2.12 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 345 TYR 0.011 0.001 TYR B 391 PHE 0.016 0.002 PHE A 468 TRP 0.012 0.002 TRP B 104 HIS 0.003 0.001 HIS A 141 Details of bonding type rmsd covalent geometry : bond 0.00418 ( 8970) covalent geometry : angle 0.64499 (12156) hydrogen bonds : bond 0.04957 ( 601) hydrogen bonds : angle 4.13834 ( 1773) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 149 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 214 ARG cc_start: 0.8847 (OUTLIER) cc_final: 0.8197 (mtm-85) REVERT: A 268 TYR cc_start: 0.5794 (t80) cc_final: 0.5056 (t80) REVERT: A 271 MET cc_start: 0.7080 (tmm) cc_final: 0.6776 (tmm) REVERT: A 272 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.7241 (mp10) REVERT: A 316 ARG cc_start: 0.8862 (OUTLIER) cc_final: 0.7543 (mmm-85) REVERT: A 391 TYR cc_start: 0.9225 (m-80) cc_final: 0.8920 (m-80) REVERT: A 449 GLU cc_start: 0.8834 (mm-30) cc_final: 0.8501 (mt-10) REVERT: A 460 PHE cc_start: 0.7346 (m-80) cc_final: 0.7086 (m-80) REVERT: A 525 MET cc_start: 0.5942 (tpt) cc_final: 0.5624 (tpt) REVERT: A 559 THR cc_start: 0.8248 (OUTLIER) cc_final: 0.7949 (p) REVERT: B 171 LEU cc_start: 0.7401 (OUTLIER) cc_final: 0.5938 (tt) REVERT: B 259 MET cc_start: 0.7641 (tmm) cc_final: 0.7177 (tmm) REVERT: B 271 MET cc_start: 0.7656 (mtp) cc_final: 0.7249 (ttm) REVERT: B 286 PHE cc_start: 0.8361 (OUTLIER) cc_final: 0.7799 (m-80) REVERT: B 317 MET cc_start: 0.8559 (mtp) cc_final: 0.8249 (mtp) REVERT: B 430 THR cc_start: 0.8661 (OUTLIER) cc_final: 0.8210 (t) REVERT: B 478 MET cc_start: 0.8907 (tpp) cc_final: 0.8663 (mmt) REVERT: B 536 ARG cc_start: 0.8283 (ptm160) cc_final: 0.7796 (ptm160) outliers start: 49 outliers final: 32 residues processed: 182 average time/residue: 0.0896 time to fit residues: 23.2962 Evaluate side-chains 181 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 142 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 272 GLN Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 316 ARG Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 437 TYR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 286 PHE Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 559 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 88 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 113 optimal weight: 9.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.158643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.123590 restraints weight = 14708.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.128030 restraints weight = 7333.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.130762 restraints weight = 4879.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.132325 restraints weight = 3873.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.132915 restraints weight = 3413.812| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8970 Z= 0.150 Angle : 0.618 10.395 12156 Z= 0.314 Chirality : 0.042 0.252 1468 Planarity : 0.005 0.059 1514 Dihedral : 8.377 80.323 1288 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.63 % Favored : 94.28 % Rotamer: Outliers : 4.27 % Allowed : 26.35 % Favored : 69.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 1.16 (0.26), residues: 1136 helix: 2.03 (0.19), residues: 766 sheet: -1.20 (0.68), residues: 44 loop : -2.15 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 345 TYR 0.009 0.001 TYR B 391 PHE 0.024 0.002 PHE A 75 TRP 0.007 0.001 TRP A 104 HIS 0.003 0.001 HIS A 141 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 8970) covalent geometry : angle 0.61845 (12156) hydrogen bonds : bond 0.04736 ( 601) hydrogen bonds : angle 4.06653 ( 1773) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 143 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 214 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.8155 (mtm-85) REVERT: A 268 TYR cc_start: 0.5813 (t80) cc_final: 0.5108 (t80) REVERT: A 271 MET cc_start: 0.7027 (tmm) cc_final: 0.6773 (tmm) REVERT: A 272 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.7136 (mp10) REVERT: A 316 ARG cc_start: 0.8844 (OUTLIER) cc_final: 0.7544 (mmm-85) REVERT: A 391 TYR cc_start: 0.9216 (m-80) cc_final: 0.8929 (m-80) REVERT: A 433 GLU cc_start: 0.7796 (tm-30) cc_final: 0.7564 (tm-30) REVERT: A 449 GLU cc_start: 0.8819 (mm-30) cc_final: 0.8476 (mt-10) REVERT: A 460 PHE cc_start: 0.7316 (m-80) cc_final: 0.7065 (m-80) REVERT: A 525 MET cc_start: 0.5989 (tpt) cc_final: 0.5679 (tpt) REVERT: A 559 THR cc_start: 0.8248 (OUTLIER) cc_final: 0.7944 (p) REVERT: B 243 GLU cc_start: 0.8265 (tm-30) cc_final: 0.7797 (tm-30) REVERT: B 259 MET cc_start: 0.7645 (tmm) cc_final: 0.7164 (tmm) REVERT: B 271 MET cc_start: 0.7570 (mtp) cc_final: 0.7213 (ttm) REVERT: B 286 PHE cc_start: 0.8321 (OUTLIER) cc_final: 0.7834 (m-80) REVERT: B 317 MET cc_start: 0.8519 (mtp) cc_final: 0.8262 (mtp) REVERT: B 430 THR cc_start: 0.8703 (OUTLIER) cc_final: 0.8270 (t) REVERT: B 478 MET cc_start: 0.8860 (tpp) cc_final: 0.8622 (mmt) REVERT: B 536 ARG cc_start: 0.8274 (ptm160) cc_final: 0.7784 (ptm160) outliers start: 41 outliers final: 32 residues processed: 169 average time/residue: 0.0946 time to fit residues: 22.5065 Evaluate side-chains 175 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 137 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 272 GLN Chi-restraints excluded: chain A residue 316 ARG Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 437 TYR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 286 PHE Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 559 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 4 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 90 optimal weight: 9.9990 chunk 9 optimal weight: 0.6980 chunk 86 optimal weight: 3.9990 chunk 44 optimal weight: 0.0770 chunk 53 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.160357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.125563 restraints weight = 14652.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.130110 restraints weight = 7133.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.132962 restraints weight = 4694.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.134619 restraints weight = 3694.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.135373 restraints weight = 3234.056| |-----------------------------------------------------------------------------| r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8970 Z= 0.132 Angle : 0.608 10.586 12156 Z= 0.306 Chirality : 0.041 0.256 1468 Planarity : 0.004 0.058 1514 Dihedral : 8.279 81.058 1288 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.19 % Favored : 94.72 % Rotamer: Outliers : 4.06 % Allowed : 27.08 % Favored : 68.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 1.20 (0.26), residues: 1136 helix: 2.03 (0.19), residues: 768 sheet: -1.01 (0.69), residues: 44 loop : -2.09 (0.32), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 201 TYR 0.007 0.001 TYR B 391 PHE 0.018 0.002 PHE B 160 TRP 0.006 0.001 TRP A 104 HIS 0.003 0.001 HIS A 141 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 8970) covalent geometry : angle 0.60799 (12156) hydrogen bonds : bond 0.04437 ( 601) hydrogen bonds : angle 3.98704 ( 1773) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 146 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 214 ARG cc_start: 0.8785 (OUTLIER) cc_final: 0.8162 (mtm-85) REVERT: A 268 TYR cc_start: 0.5802 (t80) cc_final: 0.5100 (t80) REVERT: A 271 MET cc_start: 0.7023 (tmm) cc_final: 0.6768 (tmm) REVERT: A 272 GLN cc_start: 0.8629 (OUTLIER) cc_final: 0.7038 (mp10) REVERT: A 316 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.7478 (mmm-85) REVERT: A 342 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.7798 (tt0) REVERT: A 388 GLU cc_start: 0.8793 (tp30) cc_final: 0.8592 (tp30) REVERT: A 391 TYR cc_start: 0.9215 (m-80) cc_final: 0.8925 (m-80) REVERT: A 433 GLU cc_start: 0.7768 (tm-30) cc_final: 0.7523 (tm-30) REVERT: A 449 GLU cc_start: 0.8811 (mm-30) cc_final: 0.8467 (mt-10) REVERT: A 460 PHE cc_start: 0.7287 (m-80) cc_final: 0.7038 (m-80) REVERT: A 525 MET cc_start: 0.5938 (tpt) cc_final: 0.5687 (tpt) REVERT: A 559 THR cc_start: 0.8228 (OUTLIER) cc_final: 0.7917 (p) REVERT: B 243 GLU cc_start: 0.8251 (tm-30) cc_final: 0.7800 (tm-30) REVERT: B 259 MET cc_start: 0.7689 (tmm) cc_final: 0.7203 (tmm) REVERT: B 271 MET cc_start: 0.7623 (mtp) cc_final: 0.7230 (ttm) REVERT: B 286 PHE cc_start: 0.8292 (OUTLIER) cc_final: 0.7817 (m-80) REVERT: B 317 MET cc_start: 0.8486 (mtp) cc_final: 0.8231 (mtp) REVERT: B 430 THR cc_start: 0.8739 (p) cc_final: 0.8286 (t) REVERT: B 478 MET cc_start: 0.8848 (tpp) cc_final: 0.8597 (mmt) REVERT: B 536 ARG cc_start: 0.8288 (ptm160) cc_final: 0.7809 (ptm160) outliers start: 39 outliers final: 29 residues processed: 173 average time/residue: 0.0943 time to fit residues: 23.0648 Evaluate side-chains 176 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 141 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 272 GLN Chi-restraints excluded: chain A residue 316 ARG Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 437 TYR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 286 PHE Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 559 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 9 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 99 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 103 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.159906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.125384 restraints weight = 14128.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.129792 restraints weight = 6851.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.132540 restraints weight = 4464.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.134122 restraints weight = 3502.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.134877 restraints weight = 3065.671| |-----------------------------------------------------------------------------| r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 8970 Z= 0.142 Angle : 0.630 13.566 12156 Z= 0.317 Chirality : 0.042 0.257 1468 Planarity : 0.004 0.058 1514 Dihedral : 8.262 81.885 1288 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.19 % Favored : 94.72 % Rotamer: Outliers : 4.38 % Allowed : 26.46 % Favored : 69.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 1.20 (0.26), residues: 1136 helix: 2.02 (0.19), residues: 768 sheet: -0.83 (0.70), residues: 44 loop : -2.09 (0.32), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 345 TYR 0.007 0.001 TYR B 391 PHE 0.024 0.002 PHE A 75 TRP 0.006 0.001 TRP B 104 HIS 0.004 0.001 HIS A 141 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 8970) covalent geometry : angle 0.62985 (12156) hydrogen bonds : bond 0.04469 ( 601) hydrogen bonds : angle 4.00798 ( 1773) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1557.42 seconds wall clock time: 27 minutes 39.37 seconds (1659.37 seconds total)