Starting phenix.real_space_refine on Sun Apr 27 20:09:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yzb_39688/04_2025/8yzb_39688.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yzb_39688/04_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_39688/04_2025/8yzb_39688.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yzb_39688/04_2025/8yzb_39688.map" model { file = "/net/cci-nas-00/data/ceres_data/8yzb_39688/04_2025/8yzb_39688.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yzb_39688/04_2025/8yzb_39688.cif" } resolution = 3.29 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= -0.011 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 6.74, per 1000 atoms: 1.05 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: 1.57 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 0.60 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: 1.72 Time building geometry restraints manager: 1.82 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: 1.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.390 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.620 ------------------------------------------------------------------------------- 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 (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: -0.85 (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 TRP 0.003 0.000 TRP B 302 HIS 0.002 0.000 HIS B 374 PHE 0.009 0.001 PHE B 40 TYR 0.012 0.001 TYR B 41 ARG 0.002 0.000 ARG B 169 Details of bonding type rmsd hydrogen bonds : bond 0.18763 ( 304) hydrogen bonds : angle 5.31991 ( 844) SS BOND : bond 0.00131 ( 6) SS BOND : angle 0.51004 ( 12) covalent geometry : bond 0.00337 ( 6639) covalent geometry : angle 0.54484 ( 9025) *********************** 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 : 0.711 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: 0.8195 (mtp) outliers start: 10 outliers final: 2 residues processed: 165 average time/residue: 0.2202 time to fit residues: 45.9744 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 : 0.765 ------------------------------------------------------------------------------- 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 65 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 0.2980 chunk 61 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.2929 r_free = 0.2929 target = 0.052502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.044459 restraints weight = 53312.194| |-----------------------------------------------------------------------------| r_work (start): 0.2697 rms_B_bonded: 3.72 r_work: 0.2580 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2581 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2581 r_free = 0.2581 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 = 0.2581 r_free = 0.2581 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2581 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.4626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 6645 Z= 0.176 Angle : 0.681 9.535 9037 Z= 0.364 Chirality : 0.047 0.299 936 Planarity : 0.004 0.030 1170 Dihedral : 4.893 45.393 864 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.30 % Allowed : 10.19 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 0.16 (0.29), residues: 791 helix: 0.98 (0.26), residues: 382 sheet: 1.36 (0.68), residues: 50 loop : -1.04 (0.32), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 473 HIS 0.005 0.002 HIS B 228 PHE 0.019 0.003 PHE B 369 TYR 0.018 0.002 TYR B 385 ARG 0.007 0.001 ARG B 177 Details of bonding type rmsd hydrogen bonds : bond 0.05569 ( 304) hydrogen bonds : angle 4.40099 ( 844) SS BOND : bond 0.00433 ( 6) SS BOND : angle 2.34167 ( 12) covalent geometry : bond 0.00393 ( 6639) covalent geometry : angle 0.67582 ( 9025) *********************** 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 114 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 340 GLU cc_start: 0.8608 (tp30) cc_final: 0.8310 (tp30) REVERT: A 493 GLN cc_start: 0.9026 (OUTLIER) cc_final: 0.8791 (mp10) outliers start: 16 outliers final: 7 residues processed: 108 average time/residue: 0.1956 time to fit residues: 28.1290 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 : 0.756 ------------------------------------------------------------------------------- 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 512 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 0 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.2778 r_free = 0.2778 target = 0.046798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2544 r_free = 0.2544 target = 0.039047 restraints weight = 54117.235| |-----------------------------------------------------------------------------| r_work (start): 0.2541 rms_B_bonded: 3.52 r_work: 0.2423 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2423 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2424 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2424 r_free = 0.2424 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2424 r_free = 0.2424 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2424 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8961 moved from start: 0.6153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 6645 Z= 0.242 Angle : 0.748 13.485 9037 Z= 0.405 Chirality : 0.051 0.338 936 Planarity : 0.005 0.030 1170 Dihedral : 5.253 46.352 863 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.73 % Allowed : 11.48 % 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 (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: -0.04 (0.29), residues: 791 helix: 0.71 (0.26), residues: 394 sheet: 1.75 (0.72), residues: 48 loop : -1.13 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 473 HIS 0.008 0.002 HIS B 374 PHE 0.028 0.003 PHE B 369 TYR 0.026 0.002 TYR B 385 ARG 0.008 0.001 ARG B 177 Details of bonding type rmsd hydrogen bonds : bond 0.07872 ( 304) hydrogen bonds : angle 4.69756 ( 844) SS BOND : bond 0.00914 ( 6) SS BOND : angle 3.37626 ( 12) covalent geometry : bond 0.00576 ( 6639) covalent geometry : angle 0.73811 ( 9025) *********************** 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 97 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 GLU cc_start: 0.8847 (tp30) cc_final: 0.8540 (tp30) REVERT: A 347 PHE cc_start: 0.9044 (OUTLIER) cc_final: 0.8397 (m-80) REVERT: B 203 TRP cc_start: 0.9200 (OUTLIER) cc_final: 0.8594 (m-10) REVERT: B 383 MET cc_start: 0.9055 (ttm) cc_final: 0.8332 (mtp) REVERT: B 512 PHE cc_start: 0.8573 (OUTLIER) cc_final: 0.7913 (t80) outliers start: 19 outliers final: 10 residues processed: 91 average time/residue: 0.1963 time to fit residues: 23.8174 Evaluate side-chains 80 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 PHE 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 6 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 5 optimal weight: 4.9990 chunk 59 optimal weight: 0.2980 chunk 58 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 228 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.048443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2576 r_free = 0.2576 target = 0.040275 restraints weight = 62892.653| |-----------------------------------------------------------------------------| r_work (start): 0.2572 rms_B_bonded: 4.16 r_work: 0.2445 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2445 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2445 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2445 r_free = 0.2445 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2445 r_free = 0.2445 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2445 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 moved from start: 0.6241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 6645 Z= 0.151 Angle : 0.637 16.287 9037 Z= 0.339 Chirality : 0.046 0.304 936 Planarity : 0.004 0.034 1170 Dihedral : 5.055 45.794 863 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.01 % Allowed : 10.90 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: 0.29 (0.29), residues: 791 helix: 1.04 (0.26), residues: 393 sheet: 1.69 (0.72), residues: 52 loop : -1.03 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 473 HIS 0.004 0.001 HIS B 228 PHE 0.019 0.002 PHE B 369 TYR 0.015 0.001 TYR B 385 ARG 0.003 0.000 ARG B 177 Details of bonding type rmsd hydrogen bonds : bond 0.05771 ( 304) hydrogen bonds : angle 4.40114 ( 844) SS BOND : bond 0.00790 ( 6) SS BOND : angle 2.49117 ( 12) covalent geometry : bond 0.00349 ( 6639) covalent geometry : angle 0.63120 ( 9025) *********************** 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 93 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 72 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 GLU cc_start: 0.8965 (tp30) cc_final: 0.8679 (tp30) REVERT: A 347 PHE cc_start: 0.8935 (OUTLIER) cc_final: 0.8137 (m-80) REVERT: A 364 ASP cc_start: 0.8768 (t0) cc_final: 0.8022 (p0) REVERT: A 471 GLU cc_start: 0.9040 (mm-30) cc_final: 0.8822 (mm-30) REVERT: B 203 TRP cc_start: 0.9124 (OUTLIER) cc_final: 0.8416 (m-10) REVERT: B 512 PHE cc_start: 0.8444 (OUTLIER) cc_final: 0.7432 (t80) REVERT: B 610 TRP cc_start: 0.9202 (t60) cc_final: 0.8950 (t60) outliers start: 21 outliers final: 8 residues processed: 84 average time/residue: 0.2007 time to fit residues: 22.5876 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 : 0.785 ------------------------------------------------------------------------------- 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 175 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 607 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 73 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 38 optimal weight: 0.4980 chunk 59 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 13 optimal weight: 0.2980 chunk 3 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 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 = 0.2824 r_free = 0.2824 target = 0.048483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2588 r_free = 0.2588 target = 0.040521 restraints weight = 58395.681| |-----------------------------------------------------------------------------| r_work (start): 0.2584 rms_B_bonded: 3.93 r_work: 0.2460 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2460 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2463 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2463 r_free = 0.2463 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 = 0.2463 r_free = 0.2463 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2463 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 moved from start: 0.6293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6645 Z= 0.141 Angle : 0.662 16.274 9037 Z= 0.348 Chirality : 0.047 0.370 936 Planarity : 0.004 0.033 1170 Dihedral : 4.786 44.775 863 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.15 % Allowed : 12.34 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (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: 0.49 (0.30), residues: 791 helix: 1.19 (0.27), residues: 394 sheet: 1.62 (0.72), residues: 52 loop : -0.88 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 473 HIS 0.004 0.001 HIS B 374 PHE 0.017 0.002 PHE B 369 TYR 0.013 0.001 TYR B 50 ARG 0.004 0.000 ARG B 177 Details of bonding type rmsd hydrogen bonds : bond 0.05625 ( 304) hydrogen bonds : angle 4.29894 ( 844) SS BOND : bond 0.00949 ( 6) SS BOND : angle 4.22839 ( 12) covalent geometry : bond 0.00310 ( 6639) covalent geometry : angle 0.64433 ( 9025) *********************** 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 : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 GLU cc_start: 0.9015 (tp30) cc_final: 0.8801 (tp30) REVERT: A 347 PHE cc_start: 0.8909 (OUTLIER) cc_final: 0.8169 (m-80) REVERT: A 364 ASP cc_start: 0.8675 (t0) cc_final: 0.8081 (p0) REVERT: B 203 TRP cc_start: 0.9195 (OUTLIER) cc_final: 0.8479 (m-10) REVERT: B 512 PHE cc_start: 0.8475 (OUTLIER) cc_final: 0.7454 (t80) REVERT: B 610 TRP cc_start: 0.9122 (t60) cc_final: 0.8871 (t60) outliers start: 15 outliers final: 8 residues processed: 79 average time/residue: 0.2042 time to fit residues: 21.4116 Evaluate side-chains 74 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.761 ------------------------------------------------------------------------------- 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 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 175 GLN Chi-restraints excluded: chain B residue 203 TRP Chi-restraints excluded: chain B residue 512 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 70 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 60 optimal weight: 0.4980 chunk 21 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 12 optimal weight: 0.1980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.2831 r_free = 0.2831 target = 0.048708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2597 r_free = 0.2597 target = 0.040809 restraints weight = 58227.571| |-----------------------------------------------------------------------------| r_work (start): 0.2594 rms_B_bonded: 3.87 r_work: 0.2470 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2470 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2472 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2472 r_free = 0.2472 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 = 0.2472 r_free = 0.2472 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2472 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.6386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6645 Z= 0.139 Angle : 0.677 18.330 9037 Z= 0.355 Chirality : 0.047 0.361 936 Planarity : 0.004 0.031 1170 Dihedral : 4.733 43.695 863 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.01 % Allowed : 12.63 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (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: 0.50 (0.30), residues: 791 helix: 1.25 (0.27), residues: 394 sheet: 1.58 (0.72), residues: 52 loop : -0.95 (0.31), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 473 HIS 0.004 0.001 HIS B 374 PHE 0.016 0.001 PHE B 369 TYR 0.017 0.001 TYR B 50 ARG 0.003 0.000 ARG B 177 Details of bonding type rmsd hydrogen bonds : bond 0.05534 ( 304) hydrogen bonds : angle 4.24915 ( 844) SS BOND : bond 0.01303 ( 6) SS BOND : angle 4.59126 ( 12) covalent geometry : bond 0.00301 ( 6639) covalent geometry : angle 0.65668 ( 9025) *********************** 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 83 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 PHE cc_start: 0.8881 (OUTLIER) cc_final: 0.8060 (m-80) REVERT: A 364 ASP cc_start: 0.8669 (t0) cc_final: 0.8094 (p0) REVERT: B 203 TRP cc_start: 0.9232 (OUTLIER) cc_final: 0.8505 (m-10) REVERT: B 512 PHE cc_start: 0.8480 (OUTLIER) cc_final: 0.7457 (t80) REVERT: B 601 ASN cc_start: 0.9075 (p0) cc_final: 0.8872 (p0) REVERT: B 610 TRP cc_start: 0.9072 (t60) cc_final: 0.8837 (t60) outliers start: 14 outliers final: 9 residues processed: 78 average time/residue: 0.2050 time to fit residues: 21.4454 Evaluate side-chains 79 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.797 ------------------------------------------------------------------------------- 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 203 TRP Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 579 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 9 optimal weight: 0.0980 chunk 2 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 0 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.2810 r_free = 0.2810 target = 0.047955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2594 r_free = 0.2594 target = 0.040732 restraints weight = 33342.126| |-----------------------------------------------------------------------------| r_work (start): 0.2592 rms_B_bonded: 2.87 r_work: 0.2490 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2490 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2491 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2491 r_free = 0.2491 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2491 r_free = 0.2491 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2491 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.6499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6645 Z= 0.158 Angle : 0.701 15.232 9037 Z= 0.371 Chirality : 0.047 0.289 936 Planarity : 0.004 0.032 1170 Dihedral : 4.834 44.017 863 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.44 % Allowed : 12.77 % 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 (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: 0.40 (0.29), residues: 791 helix: 1.20 (0.27), residues: 394 sheet: 1.57 (0.74), residues: 48 loop : -1.02 (0.30), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 473 HIS 0.005 0.001 HIS B 374 PHE 0.019 0.002 PHE B 369 TYR 0.016 0.001 TYR B 50 ARG 0.005 0.000 ARG B 177 Details of bonding type rmsd hydrogen bonds : bond 0.05860 ( 304) hydrogen bonds : angle 4.31197 ( 844) SS BOND : bond 0.00882 ( 6) SS BOND : angle 4.12993 ( 12) covalent geometry : bond 0.00359 ( 6639) covalent geometry : angle 0.68491 ( 9025) *********************** 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 86 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 PHE cc_start: 0.8884 (OUTLIER) cc_final: 0.8110 (m-80) REVERT: A 364 ASP cc_start: 0.8634 (t0) cc_final: 0.8038 (p0) REVERT: B 115 ARG cc_start: 0.8183 (tpm170) cc_final: 0.7872 (tpp-160) REVERT: B 203 TRP cc_start: 0.9240 (OUTLIER) cc_final: 0.8440 (m-10) REVERT: B 512 PHE cc_start: 0.8500 (OUTLIER) cc_final: 0.7614 (t80) REVERT: B 601 ASN cc_start: 0.9035 (p0) cc_final: 0.8834 (p0) REVERT: B 610 TRP cc_start: 0.9038 (t60) cc_final: 0.8790 (t60) outliers start: 17 outliers final: 10 residues processed: 81 average time/residue: 0.2007 time to fit residues: 21.9301 Evaluate side-chains 80 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.769 ------------------------------------------------------------------------------- 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 250 ASN Chi-restraints excluded: chain B residue 512 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.9990 chunk 58 optimal weight: 0.0770 chunk 67 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 15 optimal weight: 0.1980 chunk 22 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.049094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.041593 restraints weight = 39652.744| |-----------------------------------------------------------------------------| r_work (start): 0.2617 rms_B_bonded: 3.22 r_work: 0.2508 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2508 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2510 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2510 r_free = 0.2510 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2510 r_free = 0.2510 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2510 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.6530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6645 Z= 0.136 Angle : 0.723 21.172 9037 Z= 0.377 Chirality : 0.047 0.405 936 Planarity : 0.004 0.031 1170 Dihedral : 4.693 42.856 863 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.01 % Allowed : 13.20 % Favored : 84.79 % Cbeta Deviations : 0.00 % 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: 0.55 (0.30), residues: 791 helix: 1.34 (0.27), residues: 394 sheet: 1.53 (0.73), residues: 51 loop : -0.98 (0.31), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 436 HIS 0.003 0.001 HIS B 374 PHE 0.014 0.001 PHE B 369 TYR 0.026 0.001 TYR B 50 ARG 0.003 0.000 ARG B 177 Details of bonding type rmsd hydrogen bonds : bond 0.05238 ( 304) hydrogen bonds : angle 4.18502 ( 844) SS BOND : bond 0.01131 ( 6) SS BOND : angle 4.90437 ( 12) covalent geometry : bond 0.00296 ( 6639) covalent geometry : angle 0.70071 ( 9025) *********************** 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 83 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 PHE cc_start: 0.8834 (OUTLIER) cc_final: 0.8011 (m-80) REVERT: A 364 ASP cc_start: 0.8638 (t0) cc_final: 0.8119 (p0) REVERT: B 82 MET cc_start: 0.8941 (OUTLIER) cc_final: 0.8662 (ptp) REVERT: B 115 ARG cc_start: 0.8128 (tpm170) cc_final: 0.7772 (tpp-160) REVERT: B 203 TRP cc_start: 0.9208 (OUTLIER) cc_final: 0.8371 (m-10) REVERT: B 470 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.8266 (tppp) REVERT: B 512 PHE cc_start: 0.8454 (OUTLIER) cc_final: 0.7450 (t80) REVERT: B 601 ASN cc_start: 0.9042 (p0) cc_final: 0.8834 (p0) REVERT: B 610 TRP cc_start: 0.9007 (t60) cc_final: 0.8757 (t60) outliers start: 14 outliers final: 6 residues processed: 78 average time/residue: 0.2104 time to fit residues: 21.5983 Evaluate side-chains 79 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.740 ------------------------------------------------------------------------------- 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 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 470 LYS Chi-restraints excluded: chain B residue 512 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 45 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 72 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 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 = 0.2817 r_free = 0.2817 target = 0.048152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2588 r_free = 0.2588 target = 0.040497 restraints weight = 47558.805| |-----------------------------------------------------------------------------| r_work (start): 0.2585 rms_B_bonded: 3.50 r_work: 0.2469 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2469 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2471 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2471 r_free = 0.2471 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 = 0.2471 r_free = 0.2471 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2471 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.6599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6645 Z= 0.154 Angle : 0.738 19.778 9037 Z= 0.386 Chirality : 0.047 0.368 936 Planarity : 0.004 0.037 1170 Dihedral : 4.778 42.561 863 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.01 % Allowed : 13.34 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 0.48 (0.29), residues: 791 helix: 1.27 (0.27), residues: 394 sheet: 1.71 (0.74), residues: 47 loop : -1.00 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 436 HIS 0.004 0.001 HIS B 374 PHE 0.018 0.002 PHE B 369 TYR 0.024 0.001 TYR B 50 ARG 0.003 0.000 ARG B 177 Details of bonding type rmsd hydrogen bonds : bond 0.05723 ( 304) hydrogen bonds : angle 4.26164 ( 844) SS BOND : bond 0.01135 ( 6) SS BOND : angle 4.76943 ( 12) covalent geometry : bond 0.00347 ( 6639) covalent geometry : angle 0.71793 ( 9025) *********************** 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: 14 poor density : 70 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 PHE cc_start: 0.8895 (OUTLIER) cc_final: 0.8131 (m-80) REVERT: A 364 ASP cc_start: 0.8634 (t0) cc_final: 0.8137 (p0) REVERT: B 82 MET cc_start: 0.8940 (OUTLIER) cc_final: 0.8678 (ptp) REVERT: B 203 TRP cc_start: 0.9260 (OUTLIER) cc_final: 0.8469 (m-10) REVERT: B 383 MET cc_start: 0.8845 (ttm) cc_final: 0.8107 (mtp) REVERT: B 512 PHE cc_start: 0.8497 (OUTLIER) cc_final: 0.7609 (t80) REVERT: B 601 ASN cc_start: 0.9067 (p0) cc_final: 0.8851 (p0) REVERT: B 610 TRP cc_start: 0.9042 (t60) cc_final: 0.8777 (t60) outliers start: 14 outliers final: 9 residues processed: 81 average time/residue: 0.2118 time to fit residues: 22.8504 Evaluate side-chains 82 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 PHE 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 203 TRP Chi-restraints excluded: chain B residue 250 ASN 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 52 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 64 optimal weight: 0.0270 chunk 14 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.6638 ------------------------------------------------------------------------------- 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 = 0.2819 r_free = 0.2819 target = 0.048237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2587 r_free = 0.2587 target = 0.040498 restraints weight = 52272.640| |-----------------------------------------------------------------------------| r_work (start): 0.2583 rms_B_bonded: 3.66 r_work: 0.2464 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2464 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2465 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2465 r_free = 0.2465 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 = 0.2465 r_free = 0.2465 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2465 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.6638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6645 Z= 0.154 Angle : 0.751 19.216 9037 Z= 0.391 Chirality : 0.047 0.356 936 Planarity : 0.004 0.043 1170 Dihedral : 4.788 42.610 863 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.01 % Allowed : 13.63 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 0.47 (0.30), residues: 791 helix: 1.27 (0.27), residues: 394 sheet: 1.52 (0.74), residues: 51 loop : -1.01 (0.31), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 473 HIS 0.004 0.001 HIS B 374 PHE 0.017 0.001 PHE B 369 TYR 0.025 0.001 TYR B 50 ARG 0.004 0.000 ARG B 115 Details of bonding type rmsd hydrogen bonds : bond 0.05644 ( 304) hydrogen bonds : angle 4.26473 ( 844) SS BOND : bond 0.01026 ( 6) SS BOND : angle 4.70953 ( 12) covalent geometry : bond 0.00347 ( 6639) covalent geometry : angle 0.73149 ( 9025) ********************** 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 86 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 PHE cc_start: 0.8898 (OUTLIER) cc_final: 0.8122 (m-80) REVERT: A 364 ASP cc_start: 0.8636 (t0) cc_final: 0.8142 (p0) REVERT: B 82 MET cc_start: 0.8940 (OUTLIER) cc_final: 0.8674 (ptp) REVERT: B 203 TRP cc_start: 0.9245 (OUTLIER) cc_final: 0.8435 (m-10) REVERT: B 512 PHE cc_start: 0.8489 (OUTLIER) cc_final: 0.7596 (t80) REVERT: B 601 ASN cc_start: 0.9069 (p0) cc_final: 0.8864 (p0) REVERT: B 610 TRP cc_start: 0.9029 (t60) cc_final: 0.8764 (t60) outliers start: 14 outliers final: 9 residues processed: 81 average time/residue: 0.2259 time to fit residues: 24.5073 Evaluate side-chains 83 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 PHE 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 203 TRP Chi-restraints excluded: chain B residue 250 ASN 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 47 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 58 optimal weight: 0.0000 chunk 36 optimal weight: 1.9990 chunk 9 optimal weight: 0.0470 chunk 50 optimal weight: 0.2980 chunk 64 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 overall best weight: 0.3682 ------------------------------------------------------------------------------- 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 = 0.2860 r_free = 0.2860 target = 0.049704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.042035 restraints weight = 45836.720| |-----------------------------------------------------------------------------| r_work (start): 0.2631 rms_B_bonded: 3.43 r_work: 0.2519 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2519 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2522 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2522 r_free = 0.2522 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2522 r_free = 0.2522 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2522 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.6618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6645 Z= 0.130 Angle : 0.715 18.478 9037 Z= 0.371 Chirality : 0.046 0.334 936 Planarity : 0.004 0.049 1170 Dihedral : 4.607 40.865 863 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 4.29 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 (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: 0.60 (0.30), residues: 791 helix: 1.41 (0.27), residues: 394 sheet: 1.54 (0.73), residues: 51 loop : -0.97 (0.31), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 436 HIS 0.002 0.001 HIS B 374 PHE 0.012 0.001 PHE B 369 TYR 0.026 0.001 TYR B 50 ARG 0.005 0.000 ARG B 115 Details of bonding type rmsd hydrogen bonds : bond 0.04914 ( 304) hydrogen bonds : angle 4.17327 ( 844) SS BOND : bond 0.00929 ( 6) SS BOND : angle 4.63595 ( 12) covalent geometry : bond 0.00280 ( 6639) covalent geometry : angle 0.69490 ( 9025) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3435.07 seconds wall clock time: 59 minutes 46.34 seconds (3586.34 seconds total)