Starting phenix.real_space_refine on Wed Sep 17 07:01:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yzb_39688/09_2025/8yzb_39688.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yzb_39688/09_2025/8yzb_39688.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yzb_39688/09_2025/8yzb_39688.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yzb_39688/09_2025/8yzb_39688.map" model { file = "/net/cci-nas-00/data/ceres_data/8yzb_39688/09_2025/8yzb_39688.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yzb_39688/09_2025/8yzb_39688.cif" } resolution = 3.29 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.011 sd= 0.288 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: 4 Type Number sf(0) Gaussians S 37 5.16 5 C 4137 2.51 5 N 1072 2.21 5 O 1202 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6448 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1568 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 13, 'TRANS': 181} Chain: "B" Number of atoms: 4880 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 27, 'TRANS': 569} Conformer: "B" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 27, 'TRANS': 569} bond proxies already assigned to first conformer: 4995 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AHIS B 34 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS B 34 " occ=0.50 Time building chain proxies: 2.58, per 1000 atoms: 0.40 Number of scatterers: 6448 At special positions: 0 Unit cell: (84.49, 96.39, 117.81, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 37 16.00 O 1202 8.00 N 1072 7.00 C 4137 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 141 " distance=2.03 Simple disulfide: pdb=" SG CYS B 344 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 530 " - pdb=" SG CYS B 542 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.45 Conformation dependent library (CDL) restraints added in 557.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1496 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 7 sheets defined 60.2% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 337 through 342 removed outlier: 4.198A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 364 through 366 No H-bonds generated for 'chain 'A' and resid 364 through 366' Processing helix chain 'A' and resid 367 through 372 removed outlier: 3.862A pdb=" N PHE A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 389 removed outlier: 3.589A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.811A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'B' and resid 20 through 53 removed outlier: 3.886A pdb=" N GLN B 24 " --> pdb=" O THR B 20 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N AHIS B 34 " --> pdb=" O ASP B 30 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ASP B 38 " --> pdb=" O AHIS B 34 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LEU B 39 " --> pdb=" O GLU B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 77 removed outlier: 3.534A pdb=" N VAL B 59 " --> pdb=" O THR B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.521A pdb=" N MET B 82 " --> pdb=" O LEU B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 88 removed outlier: 3.570A pdb=" N GLU B 87 " --> pdb=" O PRO B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 101 removed outlier: 3.754A pdb=" N GLN B 96 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU B 100 " --> pdb=" O GLN B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 108 removed outlier: 3.513A pdb=" N SER B 106 " --> pdb=" O ASN B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 130 Processing helix chain 'B' and resid 147 through 155 Processing helix chain 'B' and resid 157 through 194 removed outlier: 3.581A pdb=" N ARG B 161 " --> pdb=" O ASP B 157 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N TRP B 168 " --> pdb=" O ALA B 164 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG B 169 " --> pdb=" O TRP B 165 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LYS B 174 " --> pdb=" O SER B 170 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N GLN B 175 " --> pdb=" O GLU B 171 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU B 176 " --> pdb=" O VAL B 172 " (cutoff:3.500A) Proline residue: B 178 - end of helix removed outlier: 3.711A pdb=" N GLU B 181 " --> pdb=" O ARG B 177 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU B 182 " --> pdb=" O PRO B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 204 Processing helix chain 'B' and resid 205 through 208 Processing helix chain 'B' and resid 220 through 231 removed outlier: 3.588A pdb=" N GLU B 224 " --> pdb=" O GLY B 220 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU B 231 " --> pdb=" O GLU B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 252 removed outlier: 3.645A pdb=" N ASN B 250 " --> pdb=" O ALA B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 267 No H-bonds generated for 'chain 'B' and resid 265 through 267' Processing helix chain 'B' and resid 275 through 277 No H-bonds generated for 'chain 'B' and resid 275 through 277' Processing helix chain 'B' and resid 278 through 283 Processing helix chain 'B' and resid 293 through 301 Processing helix chain 'B' and resid 303 through 317 Processing helix chain 'B' and resid 324 through 331 removed outlier: 4.181A pdb=" N TRP B 328 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU B 329 " --> pdb=" O GLN B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 385 removed outlier: 3.650A pdb=" N TYR B 385 " --> pdb=" O TYR B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 388 No H-bonds generated for 'chain 'B' and resid 386 through 388' Processing helix chain 'B' and resid 389 through 393 Processing helix chain 'B' and resid 399 through 413 removed outlier: 3.744A pdb=" N MET B 408 " --> pdb=" O VAL B 404 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER B 409 " --> pdb=" O GLY B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 421 Processing helix chain 'B' and resid 431 through 447 removed outlier: 3.552A pdb=" N THR B 445 " --> pdb=" O LYS B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 466 removed outlier: 4.326A pdb=" N PHE B 452 " --> pdb=" O GLY B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 471 No H-bonds generated for 'chain 'B' and resid 469 through 471' Processing helix chain 'B' and resid 472 through 485 Processing helix chain 'B' and resid 499 through 502 Processing helix chain 'B' and resid 503 through 508 Processing helix chain 'B' and resid 512 through 533 removed outlier: 4.011A pdb=" N TYR B 516 " --> pdb=" O PHE B 512 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N PHE B 523 " --> pdb=" O THR B 519 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLN B 524 " --> pdb=" O LEU B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 542 removed outlier: 3.718A pdb=" N LYS B 541 " --> pdb=" O PRO B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 559 removed outlier: 3.852A pdb=" N GLY B 551 " --> pdb=" O SER B 547 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N MET B 557 " --> pdb=" O LYS B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 564 removed outlier: 3.984A pdb=" N GLU B 564 " --> pdb=" O GLY B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 575 Processing helix chain 'B' and resid 581 through 600 Proline residue: B 590 - end of helix removed outlier: 3.876A pdb=" N LYS B 596 " --> pdb=" O PHE B 592 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASP B 597 " --> pdb=" O THR B 593 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN B 598 " --> pdb=" O TRP B 594 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.934A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.734A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 132 through 134 removed outlier: 5.736A pdb=" N GLU B 140 " --> pdb=" O ASN B 134 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 262 through 263 removed outlier: 5.902A pdb=" N LEU B 262 " --> pdb=" O VAL B 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 347 through 352 removed outlier: 5.944A pdb=" N ASP B 355 " --> pdb=" O LEU B 351 " (cutoff:3.500A) 304 hydrogen bonds defined for protein. 844 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.16 Time building geometry restraints manager: 0.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1071 1.30 - 1.43: 1872 1.43 - 1.55: 3638 1.55 - 1.68: 0 1.68 - 1.81: 58 Bond restraints: 6639 Sorted by residual: bond pdb=" CA ASP B 38 " pdb=" C ASP B 38 " ideal model delta sigma weight residual 1.523 1.441 0.083 1.30e-02 5.92e+03 4.05e+01 bond pdb=" C PHE B 40 " pdb=" O PHE B 40 " ideal model delta sigma weight residual 1.236 1.173 0.064 1.15e-02 7.56e+03 3.05e+01 bond pdb=" C LEU B 39 " pdb=" O LEU B 39 " ideal model delta sigma weight residual 1.236 1.170 0.067 1.29e-02 6.01e+03 2.66e+01 bond pdb=" CA PHE B 40 " pdb=" CB PHE B 40 " ideal model delta sigma weight residual 1.530 1.452 0.078 1.57e-02 4.06e+03 2.46e+01 bond pdb=" N LEU B 39 " pdb=" CA LEU B 39 " ideal model delta sigma weight residual 1.458 1.394 0.064 1.30e-02 5.92e+03 2.39e+01 ... (remaining 6634 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 8916 2.05 - 4.09: 95 4.09 - 6.14: 10 6.14 - 8.18: 1 8.18 - 10.23: 3 Bond angle restraints: 9025 Sorted by residual: angle pdb=" N ASP B 38 " pdb=" CA ASP B 38 " pdb=" C ASP B 38 " ideal model delta sigma weight residual 111.28 121.51 -10.23 1.09e+00 8.42e-01 8.80e+01 angle pdb=" C LEU B 39 " pdb=" CA LEU B 39 " pdb=" CB LEU B 39 " ideal model delta sigma weight residual 110.38 119.20 -8.82 2.04e+00 2.40e-01 1.87e+01 angle pdb=" N LEU B 39 " pdb=" CA LEU B 39 " pdb=" C LEU B 39 " ideal model delta sigma weight residual 112.23 106.82 5.41 1.26e+00 6.30e-01 1.85e+01 angle pdb=" C ASP B 38 " pdb=" CA ASP B 38 " pdb=" CB ASP B 38 " ideal model delta sigma weight residual 110.79 104.00 6.79 1.66e+00 3.63e-01 1.67e+01 angle pdb=" N ASN A 370 " pdb=" CA ASN A 370 " pdb=" C ASN A 370 " ideal model delta sigma weight residual 111.69 106.77 4.92 1.23e+00 6.61e-01 1.60e+01 ... (remaining 9020 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.50: 3750 12.50 - 25.00: 128 25.00 - 37.51: 21 37.51 - 50.01: 10 50.01 - 62.51: 4 Dihedral angle restraints: 3913 sinusoidal: 1582 harmonic: 2331 Sorted by residual: dihedral pdb=" C LEU B 39 " pdb=" N LEU B 39 " pdb=" CA LEU B 39 " pdb=" CB LEU B 39 " ideal model delta harmonic sigma weight residual -122.60 -132.48 9.88 0 2.50e+00 1.60e-01 1.56e+01 dihedral pdb=" CA PHE A 347 " pdb=" C PHE A 347 " pdb=" N ALA A 348 " pdb=" CA ALA A 348 " ideal model delta harmonic sigma weight residual 180.00 164.16 15.84 0 5.00e+00 4.00e-02 1.00e+01 dihedral pdb=" CA ARG A 498 " pdb=" CB ARG A 498 " pdb=" CG ARG A 498 " pdb=" CD ARG A 498 " ideal model delta sinusoidal sigma weight residual 180.00 122.94 57.06 3 1.50e+01 4.44e-03 9.43e+00 ... (remaining 3910 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 907 0.099 - 0.199: 25 0.199 - 0.298: 2 0.298 - 0.397: 1 0.397 - 0.497: 1 Chirality restraints: 936 Sorted by residual: chirality pdb=" CA LEU B 39 " pdb=" N LEU B 39 " pdb=" C LEU B 39 " pdb=" CB LEU B 39 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.17e+00 chirality pdb=" CA ASP B 38 " pdb=" N ASP B 38 " pdb=" C ASP B 38 " pdb=" CB ASP B 38 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.12e+00 chirality pdb=" CA PHE A 377 " pdb=" N PHE A 377 " pdb=" C PHE A 377 " pdb=" CB PHE A 377 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.59e+00 ... (remaining 933 not shown) Planarity restraints: 1170 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 39 " 0.009 2.00e-02 2.50e+03 1.70e-02 2.90e+00 pdb=" C LEU B 39 " -0.029 2.00e-02 2.50e+03 pdb=" O LEU B 39 " 0.011 2.00e-02 2.50e+03 pdb=" N PHE B 40 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 37 " 0.007 2.00e-02 2.50e+03 1.35e-02 1.83e+00 pdb=" C GLU B 37 " -0.023 2.00e-02 2.50e+03 pdb=" O GLU B 37 " 0.009 2.00e-02 2.50e+03 pdb=" N ASP B 38 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 38 " 0.007 2.00e-02 2.50e+03 1.32e-02 1.75e+00 pdb=" C ASP B 38 " -0.023 2.00e-02 2.50e+03 pdb=" O ASP B 38 " 0.009 2.00e-02 2.50e+03 pdb=" N LEU B 39 " 0.008 2.00e-02 2.50e+03 ... (remaining 1167 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1323 2.77 - 3.31: 6066 3.31 - 3.84: 9857 3.84 - 4.37: 11463 4.37 - 4.90: 20361 Nonbonded interactions: 49070 Sorted by model distance: nonbonded pdb=" NH1 ARG B 177 " pdb=" O GLU B 495 " model vdw 2.242 3.120 nonbonded pdb=" O VAL B 364 " pdb=" OG1 THR B 365 " model vdw 2.244 3.040 nonbonded pdb=" O ILE B 151 " pdb=" OG SER B 155 " model vdw 2.310 3.040 nonbonded pdb=" OD1 ASN A 439 " pdb=" OG SER A 443 " model vdw 2.312 3.040 nonbonded pdb=" OD1 ASN B 394 " pdb=" N GLY B 395 " model vdw 2.323 3.120 ... (remaining 49065 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: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.400 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.320 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 6645 Z= 0.224 Angle : 0.545 10.226 9037 Z= 0.343 Chirality : 0.042 0.497 936 Planarity : 0.002 0.029 1170 Dihedral : 7.277 62.511 2399 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.43 % Allowed : 2.87 % Favored : 95.70 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.28), residues: 791 helix: 0.11 (0.26), residues: 382 sheet: 1.47 (0.71), residues: 45 loop : -1.55 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 169 TYR 0.012 0.001 TYR B 41 PHE 0.009 0.001 PHE B 40 TRP 0.003 0.000 TRP B 302 HIS 0.002 0.000 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 6639) covalent geometry : angle 0.54484 ( 9025) SS BOND : bond 0.00131 ( 6) SS BOND : angle 0.51004 ( 12) hydrogen bonds : bond 0.18763 ( 304) hydrogen bonds : angle 5.31991 ( 844) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 157 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 228 HIS cc_start: 0.7840 (t70) cc_final: 0.7465 (t-170) REVERT: B 462 MET cc_start: 0.8401 (mtp) cc_final: 0.8193 (mtp) outliers start: 10 outliers final: 2 residues processed: 165 average time/residue: 0.1048 time to fit residues: 21.9148 Evaluate side-chains 85 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 83 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 283 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.0870 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 HIS B B 42 GLN B 265 HIS B 340 GLN B 401 HIS B 472 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.052843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.044632 restraints weight = 51423.716| |-----------------------------------------------------------------------------| r_work (start): 0.2700 rms_B_bonded: 3.78 r_work: 0.2580 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2580 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2580 r_free = 0.2580 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2580 r_free = 0.2580 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2580 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.4329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 6645 Z= 0.164 Angle : 0.654 7.923 9037 Z= 0.346 Chirality : 0.046 0.279 936 Planarity : 0.004 0.028 1170 Dihedral : 4.627 45.472 864 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.44 % Allowed : 10.19 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.29), residues: 791 helix: 0.91 (0.26), residues: 389 sheet: 1.21 (0.68), residues: 53 loop : -1.05 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 177 TYR 0.017 0.002 TYR B 385 PHE 0.019 0.002 PHE A 338 TRP 0.020 0.002 TRP B 473 HIS 0.006 0.001 HIS B 228 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 6639) covalent geometry : angle 0.64457 ( 9025) SS BOND : bond 0.01885 ( 6) SS BOND : angle 3.07684 ( 12) hydrogen bonds : bond 0.05587 ( 304) hydrogen bonds : angle 4.37375 ( 844) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 340 GLU cc_start: 0.8518 (tp30) cc_final: 0.8237 (tp30) REVERT: A 493 GLN cc_start: 0.9031 (OUTLIER) cc_final: 0.8790 (mp10) REVERT: B 472 GLN cc_start: 0.9305 (mt0) cc_final: 0.8976 (mp10) outliers start: 17 outliers final: 8 residues processed: 108 average time/residue: 0.0803 time to fit residues: 11.7173 Evaluate side-chains 77 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 250 ASN Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 512 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 228 HIS B 508 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.046874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2545 r_free = 0.2545 target = 0.039264 restraints weight = 48573.358| |-----------------------------------------------------------------------------| r_work (start): 0.2542 rms_B_bonded: 3.36 r_work: 0.2430 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2430 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2432 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2432 r_free = 0.2432 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2432 r_free = 0.2432 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2432 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8941 moved from start: 0.6067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 6645 Z= 0.231 Angle : 0.731 11.676 9037 Z= 0.397 Chirality : 0.050 0.319 936 Planarity : 0.005 0.034 1170 Dihedral : 5.174 46.249 864 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.58 % Allowed : 11.48 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.29), residues: 791 helix: 0.77 (0.26), residues: 393 sheet: 1.76 (0.72), residues: 48 loop : -1.14 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 177 TYR 0.025 0.002 TYR B 385 PHE 0.027 0.003 PHE B 369 TRP 0.019 0.002 TRP B 473 HIS 0.007 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00545 ( 6639) covalent geometry : angle 0.72001 ( 9025) SS BOND : bond 0.01132 ( 6) SS BOND : angle 3.51267 ( 12) hydrogen bonds : bond 0.07648 ( 304) hydrogen bonds : angle 4.63619 ( 844) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 347 PHE cc_start: 0.9011 (OUTLIER) cc_final: 0.8379 (m-80) REVERT: B 203 TRP cc_start: 0.9165 (OUTLIER) cc_final: 0.8543 (m-10) REVERT: B 383 MET cc_start: 0.9017 (ttm) cc_final: 0.8297 (mtp) REVERT: B 472 GLN cc_start: 0.9340 (mt0) cc_final: 0.9029 (mp10) REVERT: B 512 PHE cc_start: 0.8570 (OUTLIER) cc_final: 0.7849 (t80) outliers start: 18 outliers final: 11 residues processed: 88 average time/residue: 0.0852 time to fit residues: 10.0643 Evaluate side-chains 84 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 203 TRP Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 607 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 24 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 59 optimal weight: 0.0870 chunk 50 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 15 optimal weight: 0.3980 chunk 61 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN B 228 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.048902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2605 r_free = 0.2605 target = 0.040973 restraints weight = 55725.142| |-----------------------------------------------------------------------------| r_work (start): 0.2601 rms_B_bonded: 3.81 r_work: 0.2479 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2479 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2481 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2481 r_free = 0.2481 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2481 r_free = 0.2481 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2481 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.6154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 6645 Z= 0.144 Angle : 0.623 15.663 9037 Z= 0.331 Chirality : 0.045 0.303 936 Planarity : 0.004 0.036 1170 Dihedral : 4.825 45.296 863 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.58 % Allowed : 11.48 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.30), residues: 791 helix: 1.14 (0.27), residues: 393 sheet: 1.61 (0.72), residues: 52 loop : -1.00 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 177 TYR 0.013 0.001 TYR B 385 PHE 0.018 0.002 PHE B 369 TRP 0.012 0.001 TRP A 436 HIS 0.005 0.001 HIS B 228 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 6639) covalent geometry : angle 0.61416 ( 9025) SS BOND : bond 0.00873 ( 6) SS BOND : angle 2.92409 ( 12) hydrogen bonds : bond 0.05472 ( 304) hydrogen bonds : angle 4.32269 ( 844) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 GLU cc_start: 0.8722 (tp30) cc_final: 0.8463 (tp30) REVERT: A 347 PHE cc_start: 0.8877 (OUTLIER) cc_final: 0.8148 (m-80) REVERT: A 364 ASP cc_start: 0.8697 (t0) cc_final: 0.7952 (p0) REVERT: B 203 TRP cc_start: 0.9142 (OUTLIER) cc_final: 0.8485 (m-10) REVERT: B 472 GLN cc_start: 0.9327 (mt0) cc_final: 0.9023 (mp10) REVERT: B 512 PHE cc_start: 0.8454 (OUTLIER) cc_final: 0.7477 (t80) REVERT: B 610 TRP cc_start: 0.9138 (t60) cc_final: 0.8900 (t60) outliers start: 18 outliers final: 7 residues processed: 83 average time/residue: 0.0956 time to fit residues: 10.4610 Evaluate side-chains 75 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 203 TRP Chi-restraints excluded: chain B residue 250 ASN Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 607 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 8 optimal weight: 0.1980 chunk 72 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.048430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2586 r_free = 0.2586 target = 0.040447 restraints weight = 58863.592| |-----------------------------------------------------------------------------| r_work (start): 0.2583 rms_B_bonded: 3.93 r_work: 0.2458 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2458 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2460 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2460 r_free = 0.2460 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2460 r_free = 0.2460 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2460 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8909 moved from start: 0.6250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6645 Z= 0.149 Angle : 0.672 15.920 9037 Z= 0.354 Chirality : 0.047 0.367 936 Planarity : 0.004 0.037 1170 Dihedral : 4.758 44.149 863 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.15 % Allowed : 11.33 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.30), residues: 791 helix: 1.24 (0.27), residues: 394 sheet: 1.61 (0.72), residues: 52 loop : -0.87 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 177 TYR 0.014 0.001 TYR B 385 PHE 0.018 0.002 PHE B 369 TRP 0.013 0.001 TRP A 436 HIS 0.005 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 6639) covalent geometry : angle 0.65195 ( 9025) SS BOND : bond 0.01160 ( 6) SS BOND : angle 4.50332 ( 12) hydrogen bonds : bond 0.05719 ( 304) hydrogen bonds : angle 4.27067 ( 844) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 340 GLU cc_start: 0.8773 (tp30) cc_final: 0.8497 (tp30) REVERT: A 347 PHE cc_start: 0.8913 (OUTLIER) cc_final: 0.8180 (m-80) REVERT: A 364 ASP cc_start: 0.8672 (t0) cc_final: 0.8014 (p0) REVERT: B 175 GLN cc_start: 0.7824 (mp10) cc_final: 0.7384 (mp10) REVERT: B 203 TRP cc_start: 0.9200 (OUTLIER) cc_final: 0.8481 (m-10) REVERT: B 472 GLN cc_start: 0.9335 (mt0) cc_final: 0.9029 (mp10) REVERT: B 512 PHE cc_start: 0.8489 (OUTLIER) cc_final: 0.7564 (t80) REVERT: B 610 TRP cc_start: 0.9121 (t60) cc_final: 0.8896 (t60) outliers start: 15 outliers final: 8 residues processed: 79 average time/residue: 0.0950 time to fit residues: 9.9965 Evaluate side-chains 77 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 203 TRP Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 579 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 3 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.048093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2589 r_free = 0.2589 target = 0.040583 restraints weight = 42482.782| |-----------------------------------------------------------------------------| r_work (start): 0.2586 rms_B_bonded: 3.25 r_work: 0.2474 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2474 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2476 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2476 r_free = 0.2476 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2476 r_free = 0.2476 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2476 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.6406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6645 Z= 0.154 Angle : 0.696 18.012 9037 Z= 0.367 Chirality : 0.048 0.357 936 Planarity : 0.004 0.037 1170 Dihedral : 4.759 44.298 863 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.15 % Allowed : 11.91 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.30), residues: 791 helix: 1.25 (0.27), residues: 394 sheet: 1.65 (0.73), residues: 48 loop : -0.87 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 177 TYR 0.019 0.001 TYR B 50 PHE 0.019 0.002 PHE B 369 TRP 0.013 0.001 TRP A 436 HIS 0.005 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 6639) covalent geometry : angle 0.67410 ( 9025) SS BOND : bond 0.01141 ( 6) SS BOND : angle 4.79061 ( 12) hydrogen bonds : bond 0.05853 ( 304) hydrogen bonds : angle 4.28417 ( 844) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 GLU cc_start: 0.8685 (tp30) cc_final: 0.8437 (tp30) REVERT: A 347 PHE cc_start: 0.8889 (OUTLIER) cc_final: 0.8119 (m-80) REVERT: A 364 ASP cc_start: 0.8669 (t0) cc_final: 0.8079 (p0) REVERT: B 203 TRP cc_start: 0.9196 (OUTLIER) cc_final: 0.8479 (m-10) REVERT: B 341 LYS cc_start: 0.8269 (mmtt) cc_final: 0.7813 (mptt) REVERT: B 472 GLN cc_start: 0.9321 (mt0) cc_final: 0.9028 (mp10) REVERT: B 512 PHE cc_start: 0.8487 (OUTLIER) cc_final: 0.7615 (t80) REVERT: B 610 TRP cc_start: 0.9090 (t60) cc_final: 0.8846 (t60) outliers start: 15 outliers final: 8 residues processed: 80 average time/residue: 0.0888 time to fit residues: 9.5048 Evaluate side-chains 78 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 203 TRP Chi-restraints excluded: chain B residue 512 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 0 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 75 optimal weight: 0.5980 chunk 45 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.048512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.041507 restraints weight = 27273.721| |-----------------------------------------------------------------------------| r_work (start): 0.2615 rms_B_bonded: 2.55 r_work: 0.2522 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.2522 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2523 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2523 r_free = 0.2523 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2523 r_free = 0.2523 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2523 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.6432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6645 Z= 0.144 Angle : 0.672 14.732 9037 Z= 0.356 Chirality : 0.046 0.276 936 Planarity : 0.004 0.037 1170 Dihedral : 4.665 43.675 863 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.30 % Allowed : 11.91 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.30), residues: 791 helix: 1.32 (0.27), residues: 394 sheet: 1.52 (0.73), residues: 52 loop : -0.91 (0.31), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 177 TYR 0.025 0.001 TYR B 50 PHE 0.017 0.001 PHE B 369 TRP 0.012 0.001 TRP A 436 HIS 0.004 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 6639) covalent geometry : angle 0.65316 ( 9025) SS BOND : bond 0.00720 ( 6) SS BOND : angle 4.35729 ( 12) hydrogen bonds : bond 0.05517 ( 304) hydrogen bonds : angle 4.24703 ( 844) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 GLU cc_start: 0.8633 (tp30) cc_final: 0.8392 (tp30) REVERT: A 347 PHE cc_start: 0.8832 (OUTLIER) cc_final: 0.8024 (m-80) REVERT: A 364 ASP cc_start: 0.8596 (t0) cc_final: 0.8024 (p0) REVERT: B 203 TRP cc_start: 0.9222 (OUTLIER) cc_final: 0.8495 (m-10) REVERT: B 341 LYS cc_start: 0.8270 (mmtt) cc_final: 0.7849 (mptt) REVERT: B 472 GLN cc_start: 0.9266 (mt0) cc_final: 0.8973 (mp10) REVERT: B 512 PHE cc_start: 0.8444 (OUTLIER) cc_final: 0.7624 (t80) REVERT: B 610 TRP cc_start: 0.9006 (t60) cc_final: 0.8773 (t60) outliers start: 16 outliers final: 10 residues processed: 80 average time/residue: 0.0966 time to fit residues: 10.2137 Evaluate side-chains 81 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 203 TRP Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 579 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 31 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.045073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2506 r_free = 0.2506 target = 0.037946 restraints weight = 35618.994| |-----------------------------------------------------------------------------| r_work (start): 0.2504 rms_B_bonded: 2.88 r_work: 0.2403 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2403 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2405 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2405 r_free = 0.2405 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2405 r_free = 0.2405 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2405 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8963 moved from start: 0.6687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 6645 Z= 0.265 Angle : 0.838 22.401 9037 Z= 0.447 Chirality : 0.053 0.441 936 Planarity : 0.005 0.037 1170 Dihedral : 5.321 47.543 863 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.30 % Allowed : 11.91 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.29), residues: 791 helix: 0.84 (0.26), residues: 393 sheet: 1.69 (0.74), residues: 50 loop : -1.13 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 177 TYR 0.025 0.002 TYR B 385 PHE 0.028 0.003 PHE B 369 TRP 0.015 0.002 TRP B 473 HIS 0.007 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00633 ( 6639) covalent geometry : angle 0.81444 ( 9025) SS BOND : bond 0.01294 ( 6) SS BOND : angle 5.44910 ( 12) hydrogen bonds : bond 0.07876 ( 304) hydrogen bonds : angle 4.64262 ( 844) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 GLU cc_start: 0.8776 (tp30) cc_final: 0.8471 (tp30) REVERT: A 347 PHE cc_start: 0.9148 (OUTLIER) cc_final: 0.8296 (m-80) REVERT: A 364 ASP cc_start: 0.8690 (t0) cc_final: 0.8099 (p0) REVERT: B 203 TRP cc_start: 0.9237 (OUTLIER) cc_final: 0.8555 (m-10) REVERT: B 383 MET cc_start: 0.8975 (ttm) cc_final: 0.8290 (mtp) REVERT: B 512 PHE cc_start: 0.8625 (OUTLIER) cc_final: 0.8158 (t80) REVERT: B 610 TRP cc_start: 0.9040 (t60) cc_final: 0.8795 (t60) outliers start: 16 outliers final: 12 residues processed: 84 average time/residue: 0.0958 time to fit residues: 10.6964 Evaluate side-chains 87 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain B residue 203 TRP Chi-restraints excluded: chain B residue 250 ASN Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 579 MET Chi-restraints excluded: chain B residue 607 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 7 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 67 optimal weight: 0.0370 chunk 38 optimal weight: 0.3980 chunk 12 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 59 optimal weight: 0.0270 chunk 27 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.048730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2599 r_free = 0.2599 target = 0.040890 restraints weight = 56616.875| |-----------------------------------------------------------------------------| r_work (start): 0.2594 rms_B_bonded: 3.80 r_work: 0.2472 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2472 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2474 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2474 r_free = 0.2474 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2474 r_free = 0.2474 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2474 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.6577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6645 Z= 0.136 Angle : 0.725 19.785 9037 Z= 0.379 Chirality : 0.046 0.353 936 Planarity : 0.004 0.038 1170 Dihedral : 4.847 45.646 863 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.58 % Allowed : 13.63 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.29), residues: 791 helix: 1.24 (0.27), residues: 391 sheet: 1.48 (0.73), residues: 51 loop : -0.97 (0.31), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 177 TYR 0.027 0.001 TYR B 50 PHE 0.014 0.001 PHE B 369 TRP 0.016 0.001 TRP A 436 HIS 0.003 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 6639) covalent geometry : angle 0.70199 ( 9025) SS BOND : bond 0.00987 ( 6) SS BOND : angle 5.01226 ( 12) hydrogen bonds : bond 0.05227 ( 304) hydrogen bonds : angle 4.24590 ( 844) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 GLU cc_start: 0.8764 (tp30) cc_final: 0.8528 (tp30) REVERT: A 347 PHE cc_start: 0.8933 (OUTLIER) cc_final: 0.8005 (m-80) REVERT: A 364 ASP cc_start: 0.8723 (t0) cc_final: 0.8152 (p0) REVERT: B 82 MET cc_start: 0.8905 (OUTLIER) cc_final: 0.8558 (mtp) REVERT: B 512 PHE cc_start: 0.8434 (OUTLIER) cc_final: 0.7563 (t80) outliers start: 11 outliers final: 6 residues processed: 81 average time/residue: 0.0969 time to fit residues: 10.4412 Evaluate side-chains 78 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 512 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 43 optimal weight: 0.0370 chunk 41 optimal weight: 0.9990 chunk 74 optimal weight: 0.1980 chunk 53 optimal weight: 0.1980 chunk 37 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.049032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2609 r_free = 0.2609 target = 0.041207 restraints weight = 55742.278| |-----------------------------------------------------------------------------| r_work (start): 0.2607 rms_B_bonded: 3.81 r_work: 0.2481 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2481 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2482 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2482 r_free = 0.2482 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2482 r_free = 0.2482 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2482 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.6586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6645 Z= 0.134 Angle : 0.712 19.142 9037 Z= 0.370 Chirality : 0.046 0.337 936 Planarity : 0.004 0.037 1170 Dihedral : 4.630 43.591 863 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.15 % Allowed : 14.20 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.30), residues: 791 helix: 1.41 (0.27), residues: 394 sheet: 1.37 (0.73), residues: 51 loop : -0.96 (0.31), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 177 TYR 0.025 0.001 TYR B 50 PHE 0.012 0.001 PHE B 369 TRP 0.013 0.001 TRP A 436 HIS 0.003 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 6639) covalent geometry : angle 0.68925 ( 9025) SS BOND : bond 0.00921 ( 6) SS BOND : angle 4.93331 ( 12) hydrogen bonds : bond 0.05108 ( 304) hydrogen bonds : angle 4.17127 ( 844) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 GLU cc_start: 0.8764 (tp30) cc_final: 0.8553 (tp30) REVERT: A 364 ASP cc_start: 0.8620 (t0) cc_final: 0.8180 (p0) REVERT: B 82 MET cc_start: 0.8941 (OUTLIER) cc_final: 0.8664 (ptp) REVERT: B 512 PHE cc_start: 0.8475 (OUTLIER) cc_final: 0.7517 (t80) outliers start: 8 outliers final: 6 residues processed: 76 average time/residue: 0.1020 time to fit residues: 10.1865 Evaluate side-chains 79 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 512 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 75 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 61 optimal weight: 0.0670 chunk 33 optimal weight: 0.8980 chunk 4 optimal weight: 0.0370 chunk 62 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.048757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2593 r_free = 0.2593 target = 0.040637 restraints weight = 77137.282| |-----------------------------------------------------------------------------| r_work (start): 0.2590 rms_B_bonded: 4.45 r_work: 0.2453 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2453 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2455 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2455 r_free = 0.2455 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2455 r_free = 0.2455 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2455 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 moved from start: 0.6602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6645 Z= 0.141 Angle : 0.715 18.764 9037 Z= 0.373 Chirality : 0.046 0.328 936 Planarity : 0.004 0.037 1170 Dihedral : 4.627 42.555 863 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.43 % Allowed : 14.06 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.30), residues: 791 helix: 1.43 (0.27), residues: 394 sheet: 1.54 (0.74), residues: 51 loop : -1.00 (0.31), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 177 TYR 0.025 0.001 TYR B 50 PHE 0.014 0.001 PHE B 369 TRP 0.014 0.001 TRP B 473 HIS 0.004 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 6639) covalent geometry : angle 0.69314 ( 9025) SS BOND : bond 0.00940 ( 6) SS BOND : angle 4.86839 ( 12) hydrogen bonds : bond 0.05310 ( 304) hydrogen bonds : angle 4.18217 ( 844) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1695.21 seconds wall clock time: 29 minutes 49.33 seconds (1789.33 seconds total)