Starting phenix.real_space_refine on Thu Feb 13 08:08:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ri1_19180/02_2025/8ri1_19180.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ri1_19180/02_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_19180/02_2025/8ri1_19180.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ri1_19180/02_2025/8ri1_19180.map" model { file = "/net/cci-nas-00/data/ceres_data/8ri1_19180/02_2025/8ri1_19180.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ri1_19180/02_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 5.48, per 1000 atoms: 0.62 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: 2.47 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.92 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: 2.71 Time building geometry restraints manager: 2.80 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.830 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.800 ------------------------------------------------------------------------------- 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 : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 158 average time/residue: 0.2007 time to fit residues: 45.3400 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 : 1.059 ------------------------------------------------------------------------------- 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: 0.4980 overall best weight: 0.7000 ------------------------------------------------------------------------------- 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 = 0.4090 r_free = 0.4090 target = 0.160656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.126729 restraints weight = 14082.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.131176 restraints weight = 6791.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.134024 restraints weight = 4410.259| |-----------------------------------------------------------------------------| r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8970 Z= 0.220 Angle : 0.676 13.286 12156 Z= 0.348 Chirality : 0.043 0.204 1468 Planarity : 0.005 0.112 1514 Dihedral : 8.709 80.670 1291 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.63 % Favored : 94.28 % Rotamer: Outliers : 3.65 % Allowed : 22.50 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (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: 1.37 (0.26), residues: 1136 helix: 2.34 (0.19), residues: 764 sheet: -2.74 (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 0.021 0.002 PHE B 286 TYR 0.009 0.001 TYR B 419 ARG 0.008 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 196 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 161 time to evaluate : 1.425 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 188 MET cc_start: 0.7663 (tpp) cc_final: 0.7353 (tpp) REVERT: A 271 MET cc_start: 0.7159 (tmm) cc_final: 0.6951 (tmm) REVERT: A 317 MET cc_start: 0.8702 (OUTLIER) cc_final: 0.7777 (mtm) REVERT: A 460 PHE cc_start: 0.7261 (m-80) cc_final: 0.6989 (m-80) REVERT: A 501 MET cc_start: 0.8490 (ptp) cc_final: 0.8242 (ptp) REVERT: A 525 MET cc_start: 0.6027 (tpt) cc_final: 0.5756 (tpt) REVERT: A 559 THR cc_start: 0.8506 (OUTLIER) cc_final: 0.8203 (p) REVERT: B 132 MET cc_start: 0.7604 (tpp) cc_final: 0.7347 (tpp) REVERT: B 210 LEU cc_start: 0.6873 (mt) cc_final: 0.5973 (mt) REVERT: B 414 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.7560 (mtt-85) REVERT: B 430 THR cc_start: 0.8838 (p) cc_final: 0.8305 (t) REVERT: B 433 GLU cc_start: 0.8204 (tm-30) cc_final: 0.7658 (tm-30) outliers start: 35 outliers final: 21 residues processed: 181 average time/residue: 0.1822 time to fit residues: 47.8645 Evaluate side-chains 173 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 149 time to evaluate : 0.964 ------------------------------------------------------------------------------- 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 174 VAL 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 445 ASP 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: 0.1980 chunk 37 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 74 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 GLN A 485 GLN ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.161334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.126974 restraints weight = 14780.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.131565 restraints weight = 7151.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.134478 restraints weight = 4671.084| |-----------------------------------------------------------------------------| r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.1811 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= 0.183 Angle : 0.603 8.891 12156 Z= 0.311 Chirality : 0.042 0.189 1468 Planarity : 0.005 0.064 1514 Dihedral : 8.529 82.202 1288 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.55 % Favored : 94.37 % Rotamer: Outliers : 4.27 % Allowed : 23.33 % Favored : 72.40 % 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: 1.33 (0.26), residues: 1136 helix: 2.27 (0.19), residues: 764 sheet: -1.77 (0.56), residues: 54 loop : -2.27 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 413 HIS 0.010 0.001 HIS A 141 PHE 0.020 0.002 PHE B 460 TYR 0.007 0.001 TYR B 268 ARG 0.007 0.001 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 212 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 171 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 188 MET cc_start: 0.7729 (tpp) cc_final: 0.7342 (tpp) REVERT: A 214 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.8152 (mtm-85) REVERT: A 315 GLU cc_start: 0.7573 (tp30) cc_final: 0.7258 (tt0) REVERT: A 460 PHE cc_start: 0.7244 (m-80) cc_final: 0.7003 (m-80) REVERT: A 559 THR cc_start: 0.8294 (OUTLIER) cc_final: 0.7947 (p) REVERT: B 132 MET cc_start: 0.7596 (tpp) cc_final: 0.7320 (tpp) REVERT: B 210 LEU cc_start: 0.7342 (mt) cc_final: 0.6439 (mt) REVERT: B 372 ILE cc_start: 0.8772 (OUTLIER) cc_final: 0.8566 (mt) REVERT: B 423 GLU cc_start: 0.7804 (pm20) cc_final: 0.7462 (pm20) REVERT: B 430 THR cc_start: 0.8745 (OUTLIER) cc_final: 0.8236 (t) REVERT: B 433 GLU cc_start: 0.8280 (tm-30) cc_final: 0.7671 (tm-30) REVERT: B 525 MET cc_start: 0.7646 (tpp) cc_final: 0.7292 (tpp) outliers start: 41 outliers final: 18 residues processed: 198 average time/residue: 0.1867 time to fit residues: 53.3491 Evaluate side-chains 176 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 154 time to evaluate : 1.030 ------------------------------------------------------------------------------- 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 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 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 559 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 127 VAL 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: 4.9990 chunk 49 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 55 optimal weight: 10.0000 chunk 25 optimal weight: 8.9990 chunk 19 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 129 ASN B 535 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.152993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.116861 restraints weight = 14862.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.121112 restraints weight = 7594.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.123778 restraints weight = 5110.295| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 8970 Z= 0.403 Angle : 0.718 8.723 12156 Z= 0.371 Chirality : 0.045 0.183 1468 Planarity : 0.005 0.063 1514 Dihedral : 9.053 89.535 1288 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.87 % Favored : 93.05 % Rotamer: Outliers : 6.67 % Allowed : 23.12 % 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: 0.83 (0.25), residues: 1136 helix: 1.86 (0.19), residues: 764 sheet: -1.98 (0.57), residues: 54 loop : -2.37 (0.33), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 104 HIS 0.006 0.001 HIS A 141 PHE 0.023 0.002 PHE A 75 TYR 0.015 0.002 TYR B 391 ARG 0.016 0.001 ARG B 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 213 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 149 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 ARG cc_start: 0.8811 (OUTLIER) cc_final: 0.8127 (mtm-85) REVERT: A 268 TYR cc_start: 0.5912 (t80) cc_final: 0.5266 (t80) REVERT: A 315 GLU cc_start: 0.7703 (tp30) cc_final: 0.7424 (tt0) REVERT: A 317 MET cc_start: 0.8730 (OUTLIER) cc_final: 0.8078 (mtm) REVERT: A 326 GLU cc_start: 0.6534 (pm20) cc_final: 0.6147 (pm20) REVERT: A 342 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.7868 (tt0) REVERT: A 372 ILE cc_start: 0.8965 (OUTLIER) cc_final: 0.8748 (mt) REVERT: A 460 PHE cc_start: 0.7469 (m-80) cc_final: 0.7187 (m-80) REVERT: A 501 MET cc_start: 0.8666 (ptp) cc_final: 0.8140 (ptp) REVERT: A 525 MET cc_start: 0.6375 (tpt) cc_final: 0.6096 (tpt) REVERT: A 559 THR cc_start: 0.8336 (OUTLIER) cc_final: 0.8009 (p) REVERT: B 132 MET cc_start: 0.7682 (tpp) cc_final: 0.7432 (tpp) REVERT: B 249 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8065 (tp) REVERT: B 286 PHE cc_start: 0.8439 (OUTLIER) cc_final: 0.7907 (m-80) REVERT: B 317 MET cc_start: 0.8516 (mtp) cc_final: 0.8292 (mtp) REVERT: B 414 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.8339 (mtt-85) REVERT: B 433 GLU cc_start: 0.8210 (tm-30) cc_final: 0.7692 (tm-30) REVERT: B 525 MET cc_start: 0.7874 (tpp) cc_final: 0.7543 (tpp) REVERT: B 536 ARG cc_start: 0.8132 (ptm160) cc_final: 0.7921 (ptm160) outliers start: 64 outliers final: 36 residues processed: 194 average time/residue: 0.1977 time to fit residues: 54.6312 Evaluate side-chains 181 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 137 time to evaluate : 0.934 ------------------------------------------------------------------------------- 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 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 294 ILE 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 439 LEU Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 110 LEU 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 447 GLU 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: 0.9980 chunk 29 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 109 optimal weight: 5.9990 chunk 105 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.4043 r_free = 0.4043 target = 0.157673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.122605 restraints weight = 14597.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.126964 restraints weight = 7336.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.129730 restraints weight = 4896.331| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.2269 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= 0.195 Angle : 0.611 9.501 12156 Z= 0.314 Chirality : 0.041 0.186 1468 Planarity : 0.005 0.061 1514 Dihedral : 8.715 84.171 1288 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.72 % Favored : 94.19 % Rotamer: Outliers : 4.69 % Allowed : 25.73 % Favored : 69.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (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: 1.13 (0.26), residues: 1136 helix: 2.10 (0.19), residues: 764 sheet: -1.81 (0.66), residues: 44 loop : -2.28 (0.32), residues: 328 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 0.013 0.002 PHE A 468 TYR 0.008 0.001 TYR B 391 ARG 0.009 0.000 ARG B 201 *********************** 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 201 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 156 time to evaluate : 1.018 Fit side-chains revert: symmetry clash REVERT: A 142 ILE cc_start: 0.8663 (tp) cc_final: 0.8440 (tp) REVERT: A 214 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.8085 (mtm-85) REVERT: A 268 TYR cc_start: 0.5925 (t80) cc_final: 0.5207 (t80) REVERT: A 272 GLN cc_start: 0.8914 (OUTLIER) cc_final: 0.8493 (mm-40) REVERT: A 286 PHE cc_start: 0.7508 (t80) cc_final: 0.7116 (t80) REVERT: A 315 GLU cc_start: 0.7615 (tp30) cc_final: 0.7409 (tt0) REVERT: A 317 MET cc_start: 0.8542 (OUTLIER) cc_final: 0.7915 (mtm) REVERT: A 342 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.7807 (tt0) REVERT: A 460 PHE cc_start: 0.7396 (m-80) cc_final: 0.7101 (m-80) REVERT: A 501 MET cc_start: 0.8641 (ptp) cc_final: 0.8121 (ptp) REVERT: A 525 MET cc_start: 0.6243 (tpt) cc_final: 0.5875 (tpt) REVERT: A 559 THR cc_start: 0.8292 (OUTLIER) cc_final: 0.7933 (p) REVERT: B 108 ILE cc_start: 0.9115 (tp) cc_final: 0.8881 (tp) REVERT: B 132 MET cc_start: 0.7534 (tpp) cc_final: 0.7275 (tpp) REVERT: B 249 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8032 (tp) REVERT: B 271 MET cc_start: 0.7669 (mtp) cc_final: 0.7317 (ttm) REVERT: B 286 PHE cc_start: 0.8324 (OUTLIER) cc_final: 0.7788 (m-80) REVERT: B 297 MET cc_start: 0.8116 (tpt) cc_final: 0.7784 (tpt) REVERT: B 317 MET cc_start: 0.8433 (mtp) cc_final: 0.8204 (mtp) REVERT: B 414 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.8228 (mtt-85) REVERT: B 430 THR cc_start: 0.8757 (OUTLIER) cc_final: 0.8220 (t) REVERT: B 433 GLU cc_start: 0.8249 (tm-30) cc_final: 0.7685 (tm-30) REVERT: B 525 MET cc_start: 0.8052 (tpp) cc_final: 0.7794 (tpp) REVERT: B 536 ARG cc_start: 0.8141 (ptm160) cc_final: 0.7922 (ptm160) outliers start: 45 outliers final: 23 residues processed: 189 average time/residue: 0.1961 time to fit residues: 52.8249 Evaluate side-chains 173 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 141 time to evaluate : 1.121 ------------------------------------------------------------------------------- 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 127 VAL 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 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 414 ARG Chi-restraints excluded: chain B residue 430 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: 9.9990 chunk 98 optimal weight: 4.9990 chunk 84 optimal weight: 9.9990 chunk 43 optimal weight: 6.9990 chunk 111 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 53 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 chunk 54 optimal weight: 0.3980 chunk 36 optimal weight: 4.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- 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 = 0.4012 r_free = 0.4012 target = 0.154875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.119298 restraints weight = 14691.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.123632 restraints weight = 7409.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.126324 restraints weight = 4948.814| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 8970 Z= 0.306 Angle : 0.650 9.136 12156 Z= 0.334 Chirality : 0.043 0.178 1468 Planarity : 0.005 0.065 1514 Dihedral : 8.900 82.806 1288 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.69 % Favored : 93.22 % Rotamer: Outliers : 5.94 % Allowed : 25.42 % Favored : 68.65 % 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: 0.97 (0.26), residues: 1136 helix: 1.95 (0.19), residues: 764 sheet: -1.83 (0.66), residues: 44 loop : -2.30 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 104 HIS 0.006 0.001 HIS A 141 PHE 0.023 0.002 PHE A 75 TYR 0.012 0.001 TYR B 391 ARG 0.008 0.001 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 201 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 144 time to evaluate : 1.518 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 142 ILE cc_start: 0.8741 (tp) cc_final: 0.8465 (tp) REVERT: A 188 MET cc_start: 0.7643 (tpp) cc_final: 0.7314 (tpp) REVERT: A 214 ARG cc_start: 0.8758 (OUTLIER) cc_final: 0.8129 (mtm-85) REVERT: A 268 TYR cc_start: 0.5945 (t80) cc_final: 0.5279 (t80) REVERT: A 271 MET cc_start: 0.7373 (tmm) cc_final: 0.7124 (tmm) REVERT: A 286 PHE cc_start: 0.7433 (t80) cc_final: 0.7132 (t80) REVERT: A 315 GLU cc_start: 0.7688 (tp30) cc_final: 0.7467 (tt0) REVERT: A 326 GLU cc_start: 0.6032 (pm20) cc_final: 0.5478 (pm20) REVERT: A 342 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.7785 (tt0) REVERT: A 460 PHE cc_start: 0.7451 (m-80) cc_final: 0.7158 (m-80) REVERT: A 501 MET cc_start: 0.8698 (ptp) cc_final: 0.8111 (ptp) REVERT: A 559 THR cc_start: 0.8285 (OUTLIER) cc_final: 0.7932 (p) REVERT: B 108 ILE cc_start: 0.9228 (OUTLIER) cc_final: 0.8986 (tp) REVERT: B 132 MET cc_start: 0.7607 (tpp) cc_final: 0.7346 (tpp) REVERT: B 249 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8118 (tp) REVERT: B 271 MET cc_start: 0.7684 (mtp) cc_final: 0.7341 (ttm) REVERT: B 286 PHE cc_start: 0.8373 (OUTLIER) cc_final: 0.7836 (m-80) REVERT: B 423 GLU cc_start: 0.7905 (pm20) cc_final: 0.7693 (pm20) REVERT: B 430 THR cc_start: 0.8748 (OUTLIER) cc_final: 0.8180 (t) REVERT: B 433 GLU cc_start: 0.8332 (tm-30) cc_final: 0.7762 (tm-30) REVERT: B 536 ARG cc_start: 0.8175 (ptm160) cc_final: 0.7949 (ptm160) outliers start: 57 outliers final: 36 residues processed: 181 average time/residue: 0.1785 time to fit residues: 47.2772 Evaluate side-chains 182 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 139 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 137 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 236 LEU Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 272 GLN Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 328 THR 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 22 THR Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 174 VAL 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 273 VAL Chi-restraints excluded: chain B residue 286 PHE Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 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: 0.9990 chunk 110 optimal weight: 0.0070 chunk 75 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 88 optimal weight: 0.5980 chunk 10 optimal weight: 0.2980 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4076 r_free = 0.4076 target = 0.160200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.125486 restraints weight = 14636.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.129994 restraints weight = 7238.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.132826 restraints weight = 4781.325| |-----------------------------------------------------------------------------| r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2594 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= 0.171 Angle : 0.605 9.658 12156 Z= 0.306 Chirality : 0.041 0.169 1468 Planarity : 0.005 0.061 1514 Dihedral : 8.500 81.427 1288 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.93 % Favored : 94.98 % Rotamer: Outliers : 4.27 % Allowed : 26.98 % Favored : 68.75 % 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: 1.16 (0.26), residues: 1136 helix: 2.08 (0.19), residues: 766 sheet: -1.51 (0.68), residues: 44 loop : -2.25 (0.32), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 104 HIS 0.004 0.001 HIS A 141 PHE 0.016 0.002 PHE B 160 TYR 0.007 0.001 TYR B 570 ARG 0.008 0.000 ARG B 201 *********************** 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: 41 poor density : 159 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 142 ILE cc_start: 0.8714 (tp) cc_final: 0.8476 (tp) REVERT: A 214 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.8104 (mtm-85) REVERT: A 268 TYR cc_start: 0.5822 (t80) cc_final: 0.5041 (t80) REVERT: A 271 MET cc_start: 0.7252 (tmm) cc_final: 0.6861 (tmm) REVERT: A 272 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.7240 (mp10) REVERT: A 286 PHE cc_start: 0.7286 (t80) cc_final: 0.6962 (t80) REVERT: A 317 MET cc_start: 0.8377 (OUTLIER) cc_final: 0.7755 (mtm) REVERT: A 326 GLU cc_start: 0.5883 (pm20) cc_final: 0.5441 (pm20) REVERT: A 342 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.7788 (tt0) REVERT: A 433 GLU cc_start: 0.7772 (tm-30) cc_final: 0.7547 (tm-30) REVERT: A 460 PHE cc_start: 0.7350 (m-80) cc_final: 0.7062 (m-80) REVERT: A 501 MET cc_start: 0.8662 (ptp) cc_final: 0.8157 (ptp) REVERT: A 525 MET cc_start: 0.6012 (tpt) cc_final: 0.5794 (tpt) REVERT: A 559 THR cc_start: 0.8189 (OUTLIER) cc_final: 0.7858 (p) REVERT: B 108 ILE cc_start: 0.9093 (OUTLIER) cc_final: 0.8837 (tp) REVERT: B 132 MET cc_start: 0.7472 (tpp) cc_final: 0.7236 (tpp) REVERT: B 243 GLU cc_start: 0.8221 (tm-30) cc_final: 0.7743 (tm-30) REVERT: B 249 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8136 (tp) REVERT: B 271 MET cc_start: 0.7657 (mtp) cc_final: 0.7297 (ttm) REVERT: B 286 PHE cc_start: 0.8290 (OUTLIER) cc_final: 0.7779 (m-80) REVERT: B 399 ARG cc_start: 0.7982 (mtt90) cc_final: 0.7672 (mtm110) REVERT: B 430 THR cc_start: 0.8719 (p) cc_final: 0.8187 (t) REVERT: B 433 GLU cc_start: 0.8277 (tm-30) cc_final: 0.7758 (tm-30) REVERT: B 525 MET cc_start: 0.7656 (mmt) cc_final: 0.7132 (tpp) REVERT: B 536 ARG cc_start: 0.8170 (ptm160) cc_final: 0.7955 (ptm160) outliers start: 41 outliers final: 23 residues processed: 184 average time/residue: 0.1925 time to fit residues: 50.1714 Evaluate side-chains 178 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 147 time to evaluate : 0.962 ------------------------------------------------------------------------------- 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 137 LEU Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 272 GLN Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 437 TYR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 108 ILE 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 330 THR Chi-restraints excluded: chain B residue 334 ILE 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: 3.9990 chunk 110 optimal weight: 0.0970 chunk 35 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 109 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 overall best weight: 0.7578 ------------------------------------------------------------------------------- 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 = 0.4076 r_free = 0.4076 target = 0.160147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.124709 restraints weight = 14820.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.129316 restraints weight = 7219.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.132185 restraints weight = 4736.561| |-----------------------------------------------------------------------------| r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.2681 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= 0.194 Angle : 0.605 11.308 12156 Z= 0.305 Chirality : 0.041 0.170 1468 Planarity : 0.005 0.060 1514 Dihedral : 8.484 81.155 1288 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.28 % Favored : 94.63 % Rotamer: Outliers : 3.85 % Allowed : 27.60 % Favored : 68.54 % 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: 1.13 (0.26), residues: 1136 helix: 2.04 (0.19), residues: 764 sheet: -1.33 (0.69), residues: 44 loop : -2.20 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 104 HIS 0.005 0.001 HIS A 141 PHE 0.024 0.002 PHE A 75 TYR 0.006 0.001 TYR B 391 ARG 0.010 0.000 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 192 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 155 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 142 ILE cc_start: 0.8756 (tp) cc_final: 0.8503 (tp) REVERT: A 214 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.8142 (mtm-85) REVERT: A 268 TYR cc_start: 0.5811 (t80) cc_final: 0.5082 (t80) REVERT: A 271 MET cc_start: 0.7252 (tmm) cc_final: 0.6960 (tmm) REVERT: A 272 GLN cc_start: 0.8733 (OUTLIER) cc_final: 0.7252 (mp10) REVERT: A 286 PHE cc_start: 0.7265 (t80) cc_final: 0.6927 (t80) REVERT: A 315 GLU cc_start: 0.7477 (tt0) cc_final: 0.7188 (tt0) REVERT: A 316 ARG cc_start: 0.8829 (OUTLIER) cc_final: 0.7515 (mmm-85) REVERT: A 317 MET cc_start: 0.8401 (OUTLIER) cc_final: 0.7728 (mtm) REVERT: A 342 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.7793 (tt0) REVERT: A 460 PHE cc_start: 0.7306 (m-80) cc_final: 0.7030 (m-80) REVERT: A 501 MET cc_start: 0.8619 (ptp) cc_final: 0.8106 (ptp) REVERT: A 525 MET cc_start: 0.5939 (tpt) cc_final: 0.5684 (tpt) REVERT: A 559 THR cc_start: 0.8199 (OUTLIER) cc_final: 0.7870 (p) REVERT: B 108 ILE cc_start: 0.9132 (tp) cc_final: 0.8875 (tp) REVERT: B 132 MET cc_start: 0.7509 (tpp) cc_final: 0.7253 (tpp) REVERT: B 271 MET cc_start: 0.7584 (mtp) cc_final: 0.7226 (ttm) REVERT: B 286 PHE cc_start: 0.8296 (OUTLIER) cc_final: 0.7841 (m-80) REVERT: B 399 ARG cc_start: 0.7924 (mtt90) cc_final: 0.7662 (mtm110) REVERT: B 423 GLU cc_start: 0.7922 (pm20) cc_final: 0.7676 (pm20) REVERT: B 430 THR cc_start: 0.8738 (p) cc_final: 0.8187 (t) REVERT: B 433 GLU cc_start: 0.8305 (tm-30) cc_final: 0.7822 (tm-30) REVERT: B 525 MET cc_start: 0.7656 (mmt) cc_final: 0.7072 (tpp) REVERT: B 536 ARG cc_start: 0.8160 (ptm160) cc_final: 0.7941 (ptm160) outliers start: 37 outliers final: 23 residues processed: 178 average time/residue: 0.1979 time to fit residues: 49.3671 Evaluate side-chains 175 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 145 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 137 LEU 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 305 THR Chi-restraints excluded: chain A residue 316 ARG 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 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 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 330 THR Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 410 LEU 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: 0.7980 chunk 109 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 90 optimal weight: 7.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.4072 r_free = 0.4072 target = 0.159583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.124429 restraints weight = 14605.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.128939 restraints weight = 7276.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.131740 restraints weight = 4821.260| |-----------------------------------------------------------------------------| r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 8970 Z= 0.211 Angle : 0.626 13.951 12156 Z= 0.310 Chirality : 0.041 0.168 1468 Planarity : 0.004 0.060 1514 Dihedral : 8.453 81.393 1288 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.63 % Favored : 94.28 % Rotamer: Outliers : 4.06 % Allowed : 27.92 % Favored : 68.02 % 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: 1.14 (0.26), residues: 1136 helix: 2.02 (0.19), residues: 766 sheet: -1.18 (0.69), residues: 44 loop : -2.18 (0.32), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 104 HIS 0.005 0.001 HIS A 141 PHE 0.019 0.001 PHE A 384 TYR 0.007 0.001 TYR B 391 ARG 0.006 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: 39 poor density : 148 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 142 ILE cc_start: 0.8742 (tp) cc_final: 0.8501 (tp) REVERT: A 214 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.8136 (mtm-85) REVERT: A 268 TYR cc_start: 0.5822 (t80) cc_final: 0.5315 (t80) REVERT: A 272 GLN cc_start: 0.8709 (OUTLIER) cc_final: 0.8162 (mp10) REVERT: A 286 PHE cc_start: 0.7278 (t80) cc_final: 0.6938 (t80) REVERT: A 315 GLU cc_start: 0.7515 (tt0) cc_final: 0.7207 (tt0) REVERT: A 316 ARG cc_start: 0.8823 (OUTLIER) cc_final: 0.7506 (mmm-85) REVERT: A 317 MET cc_start: 0.8424 (OUTLIER) cc_final: 0.7720 (mtm) REVERT: A 342 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.7785 (tt0) REVERT: A 460 PHE cc_start: 0.7342 (m-80) cc_final: 0.7074 (m-80) REVERT: A 501 MET cc_start: 0.8708 (ptp) cc_final: 0.8251 (ptp) REVERT: A 525 MET cc_start: 0.5939 (tpt) cc_final: 0.5662 (tpt) REVERT: A 559 THR cc_start: 0.8176 (OUTLIER) cc_final: 0.7842 (p) REVERT: B 108 ILE cc_start: 0.9136 (OUTLIER) cc_final: 0.8887 (tp) REVERT: B 271 MET cc_start: 0.7652 (mtp) cc_final: 0.7247 (ttm) REVERT: B 286 PHE cc_start: 0.8341 (OUTLIER) cc_final: 0.7809 (m-80) REVERT: B 430 THR cc_start: 0.8697 (p) cc_final: 0.8124 (t) REVERT: B 433 GLU cc_start: 0.8343 (tm-30) cc_final: 0.7802 (tm-30) REVERT: B 536 ARG cc_start: 0.8189 (ptm160) cc_final: 0.7963 (ptm160) outliers start: 39 outliers final: 24 residues processed: 175 average time/residue: 0.1992 time to fit residues: 48.9702 Evaluate side-chains 172 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 140 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 272 GLN Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 316 ARG 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 559 THR Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 108 ILE 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 258 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 286 PHE Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 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: 0.7980 chunk 54 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 101 optimal weight: 7.9990 chunk 59 optimal weight: 0.9990 chunk 53 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 = 0.4051 r_free = 0.4051 target = 0.159608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.123841 restraints weight = 14947.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.128207 restraints weight = 7444.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.130881 restraints weight = 4945.971| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8970 Z= 0.265 Angle : 0.655 12.837 12156 Z= 0.329 Chirality : 0.042 0.172 1468 Planarity : 0.005 0.060 1514 Dihedral : 8.586 81.794 1288 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.90 % Favored : 94.01 % Rotamer: Outliers : 3.96 % Allowed : 27.92 % Favored : 68.12 % 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: 1.07 (0.26), residues: 1136 helix: 1.98 (0.19), residues: 764 sheet: -1.17 (0.69), residues: 44 loop : -2.24 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 104 HIS 0.005 0.001 HIS A 141 PHE 0.027 0.002 PHE A 75 TYR 0.009 0.001 TYR B 391 ARG 0.007 0.001 ARG B 201 ********************** 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 183 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 145 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 142 ILE cc_start: 0.8759 (tp) cc_final: 0.8520 (tp) REVERT: A 214 ARG cc_start: 0.8763 (OUTLIER) cc_final: 0.8163 (mtm-85) REVERT: A 268 TYR cc_start: 0.5940 (t80) cc_final: 0.5313 (t80) REVERT: A 272 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.8155 (mm-40) REVERT: A 286 PHE cc_start: 0.7365 (t80) cc_final: 0.7024 (t80) REVERT: A 315 GLU cc_start: 0.7547 (tt0) cc_final: 0.7232 (tt0) REVERT: A 316 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.7525 (mmm-85) REVERT: A 317 MET cc_start: 0.8557 (OUTLIER) cc_final: 0.7892 (mtm) REVERT: A 326 GLU cc_start: 0.5997 (pm20) cc_final: 0.5482 (pm20) REVERT: A 342 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.7779 (tt0) REVERT: A 460 PHE cc_start: 0.7386 (m-80) cc_final: 0.7124 (m-80) REVERT: A 501 MET cc_start: 0.8645 (ptp) cc_final: 0.8166 (ptp) REVERT: A 525 MET cc_start: 0.5906 (tpt) cc_final: 0.5638 (tpt) REVERT: A 559 THR cc_start: 0.8198 (OUTLIER) cc_final: 0.7862 (p) REVERT: B 108 ILE cc_start: 0.9216 (OUTLIER) cc_final: 0.8982 (tp) REVERT: B 132 MET cc_start: 0.7559 (tpp) cc_final: 0.7305 (tpp) REVERT: B 271 MET cc_start: 0.7668 (mtp) cc_final: 0.7278 (ttm) REVERT: B 286 PHE cc_start: 0.8375 (OUTLIER) cc_final: 0.7845 (m-80) REVERT: B 430 THR cc_start: 0.8734 (p) cc_final: 0.8166 (t) REVERT: B 433 GLU cc_start: 0.8342 (tm-30) cc_final: 0.7775 (tm-30) REVERT: B 525 MET cc_start: 0.7753 (mmt) cc_final: 0.7237 (tpp) REVERT: B 536 ARG cc_start: 0.8179 (ptm160) cc_final: 0.7959 (ptm160) outliers start: 38 outliers final: 28 residues processed: 172 average time/residue: 0.1990 time to fit residues: 47.9043 Evaluate side-chains 175 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 139 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 272 GLN Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 316 ARG 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 26 TYR Chi-restraints excluded: chain B residue 108 ILE 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 255 SER Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 286 PHE Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 559 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 35 optimal weight: 0.0870 chunk 31 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 14 optimal weight: 0.6980 chunk 86 optimal weight: 0.8980 chunk 33 optimal weight: 8.9990 chunk 90 optimal weight: 20.0000 chunk 67 optimal weight: 1.9990 chunk 53 optimal weight: 0.0470 overall best weight: 0.5056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 434 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.164248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.129628 restraints weight = 14274.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.134001 restraints weight = 6909.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.136723 restraints weight = 4484.354| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8970 Z= 0.182 Angle : 0.632 13.145 12156 Z= 0.311 Chirality : 0.041 0.159 1468 Planarity : 0.004 0.059 1514 Dihedral : 8.310 82.151 1288 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.84 % Favored : 95.07 % Rotamer: Outliers : 3.44 % Allowed : 28.23 % Favored : 68.33 % 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: 2.04 (0.19), residues: 768 sheet: -0.91 (0.70), residues: 44 loop : -2.19 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 104 HIS 0.004 0.001 HIS A 141 PHE 0.018 0.001 PHE B 160 TYR 0.006 0.001 TYR B 26 ARG 0.006 0.000 ARG A 345 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2679.62 seconds wall clock time: 48 minutes 58.94 seconds (2938.94 seconds total)