Starting phenix.real_space_refine on Thu Mar 13 10:28:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ri1_19180/03_2025/8ri1_19180.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ri1_19180/03_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_19180/03_2025/8ri1_19180.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ri1_19180/03_2025/8ri1_19180.map" model { file = "/net/cci-nas-00/data/ceres_data/8ri1_19180/03_2025/8ri1_19180.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ri1_19180/03_2025/8ri1_19180.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.037 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.27, per 1000 atoms: 0.60 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: 2.31 Conformation dependent library (CDL) restraints added in 984.0 milliseconds 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: 0.88 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: 2.46 Time building geometry restraints manager: 2.69 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: 0.05 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: 0.350 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: 0.000 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 21.970 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.880 ------------------------------------------------------------------------------- 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= 0.887 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (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 TRP 0.005 0.001 TRP B 104 HIS 0.004 0.000 HIS A 141 PHE 0.013 0.001 PHE A 75 TYR 0.007 0.001 TYR A 83 ARG 0.001 0.000 ARG A 345 *********************** 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 : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 158 average time/residue: 0.1770 time to fit residues: 40.4062 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 : 0.910 ------------------------------------------------------------------------------- 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 96 optimal weight: 7.9990 chunk 86 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 89 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 54 optimal weight: 0.0050 chunk 66 optimal weight: 0.9990 chunk 103 optimal weight: 0.0070 overall best weight: 0.6018 ------------------------------------------------------------------------------- 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 = 0.4093 r_free = 0.4093 target = 0.160978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.127176 restraints weight = 14064.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.131591 restraints weight = 6872.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.134418 restraints weight = 4484.992| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8970 Z= 0.212 Angle : 0.671 12.353 12156 Z= 0.345 Chirality : 0.043 0.203 1468 Planarity : 0.005 0.105 1514 Dihedral : 8.677 80.373 1291 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.72 % Favored : 94.19 % Rotamer: Outliers : 3.44 % Allowed : 22.60 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.26), residues: 1136 helix: 2.36 (0.19), residues: 764 sheet: -2.73 (0.51), residues: 58 loop : -2.13 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 413 HIS 0.009 0.001 HIS A 141 PHE 0.025 0.002 PHE B 286 TYR 0.009 0.001 TYR B 419 ARG 0.010 0.001 ARG A 345 *********************** 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 195 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 162 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 188 MET cc_start: 0.7638 (tpp) cc_final: 0.7338 (tpp) REVERT: A 271 MET cc_start: 0.7162 (tmm) cc_final: 0.6953 (tmm) REVERT: A 317 MET cc_start: 0.8690 (OUTLIER) cc_final: 0.7737 (mtm) REVERT: A 460 PHE cc_start: 0.7274 (m-80) cc_final: 0.6991 (m-80) REVERT: A 501 MET cc_start: 0.8528 (ptp) cc_final: 0.8278 (ptp) REVERT: A 525 MET cc_start: 0.6044 (tpt) cc_final: 0.5768 (tpt) REVERT: A 559 THR cc_start: 0.8475 (OUTLIER) cc_final: 0.8173 (p) REVERT: B 132 MET cc_start: 0.7585 (tpp) cc_final: 0.7309 (tpp) REVERT: B 210 LEU cc_start: 0.6793 (mt) cc_final: 0.5920 (mt) REVERT: B 414 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.7519 (mtt-85) REVERT: B 430 THR cc_start: 0.8822 (p) cc_final: 0.8284 (t) REVERT: B 433 GLU cc_start: 0.8225 (tm-30) cc_final: 0.7667 (tm-30) outliers start: 33 outliers final: 19 residues processed: 182 average time/residue: 0.1820 time to fit residues: 48.5710 Evaluate side-chains 172 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 150 time to evaluate : 0.999 ------------------------------------------------------------------------------- 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 162 MET Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 250 VAL 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 421 SER Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 164 TRP 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 414 ARG 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 94 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 21 optimal weight: 0.4980 chunk 39 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 91 optimal weight: 0.0270 chunk 74 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 overall best weight: 0.8842 ------------------------------------------------------------------------------- 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 = 0.4078 r_free = 0.4078 target = 0.160724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.125661 restraints weight = 14881.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.130292 restraints weight = 7293.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.133217 restraints weight = 4788.613| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.1732 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= 0.202 Angle : 0.611 9.144 12156 Z= 0.315 Chirality : 0.042 0.183 1468 Planarity : 0.005 0.067 1514 Dihedral : 8.591 82.321 1288 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.99 % Favored : 93.93 % Rotamer: Outliers : 4.27 % Allowed : 23.23 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.26), residues: 1136 helix: 2.28 (0.19), residues: 764 sheet: -2.27 (0.47), residues: 80 loop : -2.19 (0.34), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 413 HIS 0.009 0.001 HIS A 141 PHE 0.025 0.002 PHE B 460 TYR 0.007 0.001 TYR B 391 ARG 0.006 0.000 ARG B 486 *********************** 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: 41 poor density : 166 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 188 MET cc_start: 0.7729 (tpp) cc_final: 0.7298 (tpp) REVERT: A 214 ARG cc_start: 0.8778 (OUTLIER) cc_final: 0.8143 (mtm-85) REVERT: A 315 GLU cc_start: 0.7606 (tp30) cc_final: 0.7272 (tt0) REVERT: A 460 PHE cc_start: 0.7276 (m-80) cc_final: 0.7007 (m-80) REVERT: A 546 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7854 (mp) REVERT: A 559 THR cc_start: 0.8312 (OUTLIER) cc_final: 0.7992 (p) REVERT: B 132 MET cc_start: 0.7622 (tpp) cc_final: 0.7356 (tpp) REVERT: B 210 LEU cc_start: 0.7360 (mt) cc_final: 0.6469 (mt) REVERT: B 372 ILE cc_start: 0.8790 (OUTLIER) cc_final: 0.8588 (mt) REVERT: B 430 THR cc_start: 0.8761 (OUTLIER) cc_final: 0.8257 (t) REVERT: B 433 GLU cc_start: 0.8274 (tm-30) cc_final: 0.7684 (tm-30) REVERT: B 525 MET cc_start: 0.7622 (tpp) cc_final: 0.7245 (tpp) outliers start: 41 outliers final: 21 residues processed: 191 average time/residue: 0.2010 time to fit residues: 55.7605 Evaluate side-chains 178 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 152 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 174 VAL 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 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 546 LEU 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 159 LEU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 286 PHE Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 445 ASP 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 16 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 25 optimal weight: 8.9990 chunk 19 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 15 optimal weight: 6.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.156910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.120824 restraints weight = 14737.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.125311 restraints weight = 7403.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.128133 restraints weight = 4933.009| |-----------------------------------------------------------------------------| r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8970 Z= 0.286 Angle : 0.646 9.007 12156 Z= 0.332 Chirality : 0.043 0.187 1468 Planarity : 0.005 0.060 1514 Dihedral : 8.722 87.933 1288 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.07 % Favored : 93.84 % Rotamer: Outliers : 6.77 % Allowed : 22.29 % Favored : 70.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.26), residues: 1136 helix: 2.07 (0.19), residues: 766 sheet: -1.90 (0.56), residues: 54 loop : -2.35 (0.32), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 104 HIS 0.007 0.001 HIS A 141 PHE 0.022 0.002 PHE A 75 TYR 0.011 0.001 TYR B 391 ARG 0.005 0.000 ARG A 345 *********************** 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 224 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 159 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 188 MET cc_start: 0.7889 (tpp) cc_final: 0.7292 (tpp) REVERT: A 214 ARG cc_start: 0.8824 (OUTLIER) cc_final: 0.8154 (mtm-85) REVERT: A 268 TYR cc_start: 0.5856 (t80) cc_final: 0.5239 (t80) REVERT: A 315 GLU cc_start: 0.7613 (tp30) cc_final: 0.7373 (tt0) REVERT: A 317 MET cc_start: 0.8615 (OUTLIER) cc_final: 0.7924 (mtm) REVERT: A 326 GLU cc_start: 0.6131 (pm20) cc_final: 0.5758 (pm20) REVERT: A 342 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.7811 (tt0) REVERT: A 460 PHE cc_start: 0.7414 (m-80) cc_final: 0.7153 (m-80) REVERT: A 525 MET cc_start: 0.6415 (tpt) cc_final: 0.6142 (tpt) REVERT: A 559 THR cc_start: 0.8330 (OUTLIER) cc_final: 0.8017 (p) REVERT: B 132 MET cc_start: 0.7615 (tpp) cc_final: 0.7357 (tpp) REVERT: B 249 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8056 (tp) REVERT: B 414 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.8233 (mtt-85) REVERT: B 430 THR cc_start: 0.8817 (OUTLIER) cc_final: 0.8256 (t) REVERT: B 433 GLU cc_start: 0.8222 (tm-30) cc_final: 0.7668 (tm-30) REVERT: B 525 MET cc_start: 0.7829 (tpp) cc_final: 0.7520 (tpp) outliers start: 65 outliers final: 36 residues processed: 202 average time/residue: 0.1890 time to fit residues: 54.2985 Evaluate side-chains 189 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 146 time to evaluate : 0.889 ------------------------------------------------------------------------------- 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 137 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 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 317 MET 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 41 LEU Chi-restraints excluded: chain B residue 73 VAL 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 249 LEU Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 265 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 387 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 63 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 109 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.159849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.124438 restraints weight = 14610.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.129019 restraints weight = 7227.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.131801 restraints weight = 4783.873| |-----------------------------------------------------------------------------| r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8970 Z= 0.189 Angle : 0.594 9.189 12156 Z= 0.306 Chirality : 0.041 0.174 1468 Planarity : 0.005 0.058 1514 Dihedral : 8.505 86.907 1288 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.90 % Favored : 94.01 % Rotamer: Outliers : 4.90 % Allowed : 23.75 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.26), residues: 1136 helix: 2.17 (0.19), residues: 764 sheet: -1.72 (0.66), residues: 44 loop : -2.24 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 104 HIS 0.010 0.001 HIS A 141 PHE 0.014 0.002 PHE B 160 TYR 0.007 0.001 TYR B 570 ARG 0.006 0.000 ARG A 345 *********************** 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 206 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 159 time to evaluate : 0.882 Fit side-chains revert: symmetry clash REVERT: A 188 MET cc_start: 0.7832 (tpp) cc_final: 0.7365 (tpp) REVERT: A 214 ARG cc_start: 0.8778 (OUTLIER) cc_final: 0.8151 (mtm-85) REVERT: A 268 TYR cc_start: 0.5769 (t80) cc_final: 0.5103 (t80) REVERT: A 272 GLN cc_start: 0.8893 (OUTLIER) cc_final: 0.8471 (mm-40) REVERT: A 317 MET cc_start: 0.8403 (OUTLIER) cc_final: 0.7675 (mtm) REVERT: A 326 GLU cc_start: 0.5740 (pm20) cc_final: 0.5395 (pm20) REVERT: A 342 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.7799 (tt0) REVERT: A 460 PHE cc_start: 0.7342 (m-80) cc_final: 0.7047 (m-80) REVERT: A 501 MET cc_start: 0.8593 (ptp) cc_final: 0.8068 (ptp) REVERT: A 559 THR cc_start: 0.8289 (OUTLIER) cc_final: 0.7961 (p) REVERT: B 108 ILE cc_start: 0.9079 (tp) cc_final: 0.8874 (tp) REVERT: B 132 MET cc_start: 0.7533 (tpp) cc_final: 0.7279 (tpp) REVERT: B 249 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.8080 (tp) REVERT: B 271 MET cc_start: 0.7703 (mtp) cc_final: 0.7345 (ttm) REVERT: B 423 GLU cc_start: 0.7834 (pm20) cc_final: 0.7483 (pm20) REVERT: B 430 THR cc_start: 0.8717 (p) cc_final: 0.8184 (t) REVERT: B 433 GLU cc_start: 0.8213 (tm-30) cc_final: 0.7668 (tm-30) REVERT: B 525 MET cc_start: 0.7962 (tpp) cc_final: 0.7681 (tpp) outliers start: 47 outliers final: 24 residues processed: 190 average time/residue: 0.1876 time to fit residues: 51.5403 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 : 0.938 ------------------------------------------------------------------------------- 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 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 272 GLN 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 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 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 184 ILE Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 249 LEU 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 559 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 94 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 98 optimal weight: 5.9990 chunk 84 optimal weight: 10.0000 chunk 43 optimal weight: 6.9990 chunk 111 optimal weight: 0.4980 chunk 87 optimal weight: 0.8980 chunk 53 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 chunk 54 optimal weight: 0.3980 chunk 36 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.159460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.124248 restraints weight = 14615.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.128673 restraints weight = 7246.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.131455 restraints weight = 4811.530| |-----------------------------------------------------------------------------| r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8970 Z= 0.209 Angle : 0.602 9.479 12156 Z= 0.306 Chirality : 0.041 0.175 1468 Planarity : 0.005 0.061 1514 Dihedral : 8.496 85.677 1288 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.90 % Favored : 94.01 % Rotamer: Outliers : 4.69 % Allowed : 24.90 % Favored : 70.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.26), residues: 1136 helix: 2.11 (0.19), residues: 764 sheet: -1.64 (0.67), residues: 44 loop : -2.20 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 104 HIS 0.008 0.001 HIS A 141 PHE 0.023 0.002 PHE A 75 TYR 0.008 0.001 TYR B 391 ARG 0.010 0.000 ARG B 201 *********************** 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 198 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 153 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 188 MET cc_start: 0.7899 (tpp) cc_final: 0.7420 (tpp) REVERT: A 214 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.8192 (mtm-85) REVERT: A 268 TYR cc_start: 0.5817 (t80) cc_final: 0.5138 (t80) REVERT: A 271 MET cc_start: 0.7253 (tmm) cc_final: 0.6945 (tmm) REVERT: A 317 MET cc_start: 0.8355 (OUTLIER) cc_final: 0.7617 (mtm) REVERT: A 326 GLU cc_start: 0.5563 (pm20) cc_final: 0.5258 (pm20) REVERT: A 372 ILE cc_start: 0.8827 (OUTLIER) cc_final: 0.8551 (mt) REVERT: A 460 PHE cc_start: 0.7360 (m-80) cc_final: 0.7067 (m-80) REVERT: A 501 MET cc_start: 0.8612 (ptp) cc_final: 0.8067 (ptp) REVERT: A 525 MET cc_start: 0.6129 (tpt) cc_final: 0.5889 (tpt) REVERT: A 559 THR cc_start: 0.8267 (OUTLIER) cc_final: 0.7930 (p) REVERT: B 108 ILE cc_start: 0.9127 (tp) cc_final: 0.8910 (tp) REVERT: B 132 MET cc_start: 0.7530 (tpp) cc_final: 0.7264 (tpp) REVERT: B 249 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.8132 (tp) REVERT: B 271 MET cc_start: 0.7703 (mtp) cc_final: 0.7329 (ttm) REVERT: B 430 THR cc_start: 0.8712 (OUTLIER) cc_final: 0.8178 (t) REVERT: B 433 GLU cc_start: 0.8239 (tm-30) cc_final: 0.7708 (tm-30) outliers start: 45 outliers final: 32 residues processed: 180 average time/residue: 0.1745 time to fit residues: 45.4280 Evaluate side-chains 188 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 150 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 162 MET 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 250 VAL 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 372 ILE 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 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 249 LEU 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 410 LEU Chi-restraints excluded: chain B residue 430 THR 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 30 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 20 optimal weight: 0.5980 chunk 110 optimal weight: 7.9990 chunk 75 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 79 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 88 optimal weight: 0.4980 chunk 10 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.160801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.126244 restraints weight = 14731.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.130743 restraints weight = 7286.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.133506 restraints weight = 4824.491| |-----------------------------------------------------------------------------| r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8970 Z= 0.184 Angle : 0.592 10.424 12156 Z= 0.298 Chirality : 0.041 0.163 1468 Planarity : 0.004 0.058 1514 Dihedral : 8.316 82.208 1288 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.63 % Favored : 94.28 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.26), residues: 1136 helix: 2.08 (0.19), residues: 768 sheet: -2.04 (0.70), residues: 34 loop : -2.03 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 104 HIS 0.009 0.001 HIS A 141 PHE 0.017 0.001 PHE B 160 TYR 0.006 0.001 TYR B 391 ARG 0.006 0.000 ARG A 345 *********************** 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 200 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 155 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 TYR cc_start: 0.8227 (OUTLIER) cc_final: 0.7948 (m-10) REVERT: A 188 MET cc_start: 0.7829 (tpp) cc_final: 0.7381 (tpp) REVERT: A 214 ARG cc_start: 0.8758 (OUTLIER) cc_final: 0.8151 (mtm-85) REVERT: A 268 TYR cc_start: 0.5796 (t80) cc_final: 0.5039 (t80) REVERT: A 271 MET cc_start: 0.7234 (tmm) cc_final: 0.6841 (tmm) REVERT: A 272 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.7226 (mp10) REVERT: A 297 MET cc_start: 0.8221 (tpt) cc_final: 0.7840 (tpt) REVERT: A 317 MET cc_start: 0.8252 (OUTLIER) cc_final: 0.7495 (mtm) REVERT: A 326 GLU cc_start: 0.5498 (pm20) cc_final: 0.5217 (pm20) REVERT: A 342 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.7798 (tt0) REVERT: A 372 ILE cc_start: 0.8759 (OUTLIER) cc_final: 0.8459 (mt) REVERT: A 460 PHE cc_start: 0.7329 (m-80) cc_final: 0.7049 (m-80) REVERT: A 501 MET cc_start: 0.8603 (ptp) cc_final: 0.8067 (ptp) REVERT: A 525 MET cc_start: 0.6045 (tpt) cc_final: 0.5781 (tpt) REVERT: A 559 THR cc_start: 0.8224 (OUTLIER) cc_final: 0.7918 (p) REVERT: B 108 ILE cc_start: 0.9097 (tp) cc_final: 0.8871 (tp) REVERT: B 132 MET cc_start: 0.7483 (tpp) cc_final: 0.7242 (tpp) REVERT: B 243 GLU cc_start: 0.8236 (tm-30) cc_final: 0.7784 (tm-30) REVERT: B 249 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.8095 (tp) REVERT: B 271 MET cc_start: 0.7622 (mtp) cc_final: 0.7251 (ttm) REVERT: B 423 GLU cc_start: 0.7878 (pm20) cc_final: 0.7624 (pm20) REVERT: B 430 THR cc_start: 0.8686 (p) cc_final: 0.8222 (t) REVERT: B 478 MET cc_start: 0.8844 (tpp) cc_final: 0.8642 (mmt) REVERT: B 525 MET cc_start: 0.7729 (mmt) cc_final: 0.7169 (tpp) outliers start: 45 outliers final: 29 residues processed: 184 average time/residue: 0.1808 time to fit residues: 48.1271 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 : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 137 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 372 ILE 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 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 184 ILE Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 249 LEU 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 559 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 82 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 110 optimal weight: 0.0770 chunk 35 optimal weight: 8.9990 chunk 2 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 46 optimal weight: 0.1980 chunk 50 optimal weight: 7.9990 chunk 109 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 overall best weight: 0.5340 ------------------------------------------------------------------------------- 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 = 0.4098 r_free = 0.4098 target = 0.162384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.127299 restraints weight = 14907.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.131947 restraints weight = 7377.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.134853 restraints weight = 4878.651| |-----------------------------------------------------------------------------| r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8970 Z= 0.173 Angle : 0.593 10.877 12156 Z= 0.300 Chirality : 0.041 0.231 1468 Planarity : 0.005 0.057 1514 Dihedral : 8.171 80.946 1288 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.46 % Favored : 94.45 % Rotamer: Outliers : 4.06 % Allowed : 25.73 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.26), residues: 1136 helix: 2.08 (0.19), residues: 768 sheet: -1.09 (0.68), residues: 44 loop : -2.09 (0.32), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 164 HIS 0.009 0.001 HIS A 141 PHE 0.024 0.002 PHE A 75 TYR 0.007 0.001 TYR B 570 ARG 0.012 0.001 ARG B 201 *********************** 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 195 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 156 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 188 MET cc_start: 0.7734 (tpp) cc_final: 0.7382 (tpp) REVERT: A 214 ARG cc_start: 0.8733 (OUTLIER) cc_final: 0.8135 (mtm-85) REVERT: A 268 TYR cc_start: 0.5741 (t80) cc_final: 0.5046 (t80) REVERT: A 271 MET cc_start: 0.7093 (tmm) cc_final: 0.6805 (tmm) REVERT: A 272 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.7196 (mp10) REVERT: A 317 MET cc_start: 0.8168 (OUTLIER) cc_final: 0.7421 (mtm) REVERT: A 342 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.7785 (tt0) REVERT: A 372 ILE cc_start: 0.8722 (OUTLIER) cc_final: 0.8404 (mt) REVERT: A 391 TYR cc_start: 0.9190 (m-80) cc_final: 0.8906 (m-80) REVERT: A 460 PHE cc_start: 0.7318 (m-80) cc_final: 0.7033 (m-80) REVERT: A 501 MET cc_start: 0.8620 (ptp) cc_final: 0.8181 (ptp) REVERT: A 525 MET cc_start: 0.5988 (tpt) cc_final: 0.5742 (tpt) REVERT: A 559 THR cc_start: 0.8190 (OUTLIER) cc_final: 0.7879 (p) REVERT: B 108 ILE cc_start: 0.9075 (tp) cc_final: 0.8859 (tp) REVERT: B 243 GLU cc_start: 0.8235 (tm-30) cc_final: 0.7803 (tm-30) REVERT: B 271 MET cc_start: 0.7587 (mtp) cc_final: 0.7227 (ttm) REVERT: B 430 THR cc_start: 0.8678 (OUTLIER) cc_final: 0.8234 (t) REVERT: B 478 MET cc_start: 0.8801 (tpp) cc_final: 0.8595 (mmt) outliers start: 39 outliers final: 23 residues processed: 180 average time/residue: 0.1724 time to fit residues: 44.9918 Evaluate side-chains 177 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 147 time to evaluate : 0.926 ------------------------------------------------------------------------------- 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 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 290 LEU Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain A residue 372 ILE 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 524 LEU Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 248 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 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 23 optimal weight: 0.5980 chunk 109 optimal weight: 7.9990 chunk 10 optimal weight: 0.6980 chunk 50 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 82 optimal weight: 0.4980 chunk 90 optimal weight: 7.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.4080 r_free = 0.4080 target = 0.160483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.125628 restraints weight = 14683.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.130108 restraints weight = 7302.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.132900 restraints weight = 4845.342| |-----------------------------------------------------------------------------| r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8970 Z= 0.210 Angle : 0.621 13.269 12156 Z= 0.307 Chirality : 0.041 0.182 1468 Planarity : 0.004 0.056 1514 Dihedral : 8.207 80.256 1288 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.46 % Favored : 94.45 % Rotamer: Outliers : 4.27 % Allowed : 25.31 % Favored : 70.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.26), residues: 1136 helix: 2.06 (0.19), residues: 768 sheet: -1.00 (0.69), residues: 44 loop : -2.07 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 104 HIS 0.009 0.001 HIS A 141 PHE 0.018 0.001 PHE A 384 TYR 0.007 0.001 TYR B 391 ARG 0.007 0.000 ARG A 345 *********************** 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 187 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 146 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 TYR cc_start: 0.8201 (OUTLIER) cc_final: 0.7605 (m-10) REVERT: A 188 MET cc_start: 0.7856 (tpp) cc_final: 0.7394 (tpp) REVERT: A 268 TYR cc_start: 0.5784 (t80) cc_final: 0.5089 (t80) REVERT: A 271 MET cc_start: 0.7029 (tmm) cc_final: 0.6766 (tmm) REVERT: A 272 GLN cc_start: 0.8699 (OUTLIER) cc_final: 0.7094 (mp10) REVERT: A 316 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.7473 (mmm-85) REVERT: A 342 GLN cc_start: 0.8352 (OUTLIER) cc_final: 0.7801 (tt0) REVERT: A 372 ILE cc_start: 0.8793 (OUTLIER) cc_final: 0.8508 (mt) REVERT: A 391 TYR cc_start: 0.9200 (m-80) cc_final: 0.8921 (m-80) REVERT: A 460 PHE cc_start: 0.7295 (m-80) cc_final: 0.7028 (m-80) REVERT: A 525 MET cc_start: 0.5964 (tpt) cc_final: 0.5697 (tpt) REVERT: A 559 THR cc_start: 0.8233 (OUTLIER) cc_final: 0.7923 (p) REVERT: B 108 ILE cc_start: 0.9125 (tp) cc_final: 0.8883 (tp) REVERT: B 243 GLU cc_start: 0.8242 (tm-30) cc_final: 0.7826 (tm-30) REVERT: B 271 MET cc_start: 0.7587 (mtp) cc_final: 0.7227 (ttm) REVERT: B 430 THR cc_start: 0.8706 (OUTLIER) cc_final: 0.8263 (t) outliers start: 41 outliers final: 26 residues processed: 173 average time/residue: 0.1859 time to fit residues: 46.8295 Evaluate side-chains 176 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 143 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 184 ILE 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 342 GLN Chi-restraints excluded: chain A residue 372 ILE 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 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 184 ILE 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 330 THR Chi-restraints excluded: chain B residue 334 ILE 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 32 optimal weight: 9.9990 chunk 79 optimal weight: 0.5980 chunk 54 optimal weight: 0.0370 chunk 64 optimal weight: 1.9990 chunk 81 optimal weight: 0.0770 chunk 92 optimal weight: 5.9990 chunk 113 optimal weight: 6.9990 chunk 101 optimal weight: 7.9990 chunk 59 optimal weight: 1.9990 chunk 53 optimal weight: 0.0170 chunk 19 optimal weight: 3.9990 overall best weight: 0.5456 ------------------------------------------------------------------------------- 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 = 0.4106 r_free = 0.4106 target = 0.164436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.129909 restraints weight = 14918.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.134374 restraints weight = 7381.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.137088 restraints weight = 4884.578| |-----------------------------------------------------------------------------| r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8970 Z= 0.182 Angle : 0.619 13.926 12156 Z= 0.306 Chirality : 0.041 0.193 1468 Planarity : 0.004 0.056 1514 Dihedral : 8.111 78.486 1288 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.28 % Favored : 94.63 % Rotamer: Outliers : 3.23 % Allowed : 26.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.26), residues: 1136 helix: 2.08 (0.19), residues: 768 sheet: -0.86 (0.68), residues: 44 loop : -2.06 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 104 HIS 0.008 0.001 HIS A 141 PHE 0.025 0.002 PHE A 75 TYR 0.006 0.001 TYR B 391 ARG 0.009 0.000 ARG A 345 ********************** 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 182 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 151 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 TYR cc_start: 0.8218 (OUTLIER) cc_final: 0.7561 (m-10) REVERT: A 188 MET cc_start: 0.7757 (tpp) cc_final: 0.7373 (tpp) REVERT: A 214 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.8198 (mtm-85) REVERT: A 268 TYR cc_start: 0.5765 (t80) cc_final: 0.5091 (t80) REVERT: A 271 MET cc_start: 0.7029 (tmm) cc_final: 0.6767 (tmm) REVERT: A 272 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.7002 (mp10) REVERT: A 292 GLN cc_start: 0.8317 (mt0) cc_final: 0.8069 (mt0) REVERT: A 316 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.7352 (mmm-85) REVERT: A 342 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.7784 (tt0) REVERT: A 391 TYR cc_start: 0.9217 (m-80) cc_final: 0.8929 (m-80) REVERT: A 460 PHE cc_start: 0.7323 (m-80) cc_final: 0.7052 (m-80) REVERT: A 525 MET cc_start: 0.5995 (tpt) cc_final: 0.5724 (tpt) REVERT: A 559 THR cc_start: 0.8178 (OUTLIER) cc_final: 0.7872 (p) REVERT: B 108 ILE cc_start: 0.9070 (tp) cc_final: 0.8827 (tp) REVERT: B 243 GLU cc_start: 0.8238 (tm-30) cc_final: 0.7806 (tm-30) REVERT: B 271 MET cc_start: 0.7641 (mtp) cc_final: 0.7256 (ttm) REVERT: B 286 PHE cc_start: 0.8282 (OUTLIER) cc_final: 0.7848 (m-80) REVERT: B 430 THR cc_start: 0.8689 (p) cc_final: 0.8233 (t) outliers start: 31 outliers final: 21 residues processed: 174 average time/residue: 0.1908 time to fit residues: 46.8901 Evaluate side-chains 172 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 144 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR 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 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 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 159 LEU Chi-restraints excluded: chain B residue 184 ILE 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 330 THR Chi-restraints excluded: chain B residue 334 ILE 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 35 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 23 optimal weight: 0.3980 chunk 71 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 33 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.4077 r_free = 0.4077 target = 0.161846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.127010 restraints weight = 14968.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.131344 restraints weight = 7484.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.134079 restraints weight = 4973.189| |-----------------------------------------------------------------------------| r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.2960 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= 0.240 Angle : 0.649 13.300 12156 Z= 0.323 Chirality : 0.042 0.197 1468 Planarity : 0.005 0.057 1514 Dihedral : 8.258 78.560 1288 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.55 % Favored : 94.37 % Rotamer: Outliers : 3.75 % Allowed : 26.77 % Favored : 69.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.26), residues: 1136 helix: 2.06 (0.19), residues: 766 sheet: -0.75 (0.69), residues: 44 loop : -2.05 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 104 HIS 0.007 0.001 HIS A 141 PHE 0.018 0.002 PHE B 160 TYR 0.007 0.001 TYR A 419 ARG 0.010 0.001 ARG B 201 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2750.23 seconds wall clock time: 48 minutes 46.36 seconds (2926.36 seconds total)