Starting phenix.real_space_refine on Thu Jul 2 16:54:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9x49_66534/07_2026/9x49_66534.cif Found real_map, /net/cci-nas-00/data/ceres_data/9x49_66534/07_2026/9x49_66534.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9x49_66534/07_2026/9x49_66534.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9x49_66534/07_2026/9x49_66534.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9x49_66534/07_2026/9x49_66534.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9x49_66534/07_2026/9x49_66534.map" } resolution = 3.34 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= 0.001 sd= 0.025 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 40 5.16 5 C 5830 2.51 5 N 1523 2.21 5 O 1648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9041 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4514 Classifications: {'peptide': 572} Link IDs: {'PTRANS': 20, 'TRANS': 551} Chain: "B" Number of atoms: 4527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4527 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 13, 'TRANS': 556} Time building chain proxies: 1.52, per 1000 atoms: 0.17 Number of scatterers: 9041 At special positions: 0 Unit cell: (74.304, 100.104, 139.32, 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 40 16.00 O 1648 8.00 N 1523 7.00 C 5830 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.62 Conformation dependent library (CDL) restraints added in 448.4 milliseconds 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2154 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 5 sheets defined 72.0% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 3 through 9 removed outlier: 3.641A pdb=" N TYR A 7 " --> pdb=" O LEU A 4 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS A 9 " --> pdb=" O VAL A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 11 through 42 Proline residue: A 19 - end of helix Proline residue: A 33 - end of helix Processing helix chain 'A' and resid 42 through 47 Processing helix chain 'A' and resid 48 through 98 Processing helix chain 'A' and resid 100 through 108 Processing helix chain 'A' and resid 108 through 133 removed outlier: 4.548A pdb=" N ASP A 119 " --> pdb=" O ARG A 115 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N THR A 120 " --> pdb=" O LEU A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 152 Processing helix chain 'A' and resid 154 through 201 removed outlier: 4.173A pdb=" N TRP A 158 " --> pdb=" O ARG A 154 " (cutoff:3.500A) Proline residue: A 179 - end of helix Processing helix chain 'A' and resid 201 through 208 Processing helix chain 'A' and resid 210 through 237 removed outlier: 3.723A pdb=" N ILE A 235 " --> pdb=" O LYS A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 264 Processing helix chain 'A' and resid 268 through 281 Processing helix chain 'A' and resid 282 through 311 Processing helix chain 'A' and resid 372 through 381 Processing helix chain 'A' and resid 402 through 409 Processing helix chain 'A' and resid 424 through 429 Processing helix chain 'A' and resid 437 through 448 Processing helix chain 'A' and resid 450 through 456 removed outlier: 3.565A pdb=" N GLU A 456 " --> pdb=" O ASP A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 462 Processing helix chain 'A' and resid 473 through 488 removed outlier: 4.076A pdb=" N ARG A 488 " --> pdb=" O ARG A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 518 Processing helix chain 'A' and resid 552 through 559 Processing helix chain 'A' and resid 560 through 572 removed outlier: 3.548A pdb=" N GLN A 564 " --> pdb=" O ASN A 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 19 Processing helix chain 'B' and resid 20 through 51 Proline residue: B 42 - end of helix Processing helix chain 'B' and resid 52 through 54 No H-bonds generated for 'chain 'B' and resid 52 through 54' Processing helix chain 'B' and resid 56 through 108 Proline residue: B 83 - end of helix Processing helix chain 'B' and resid 109 through 116 removed outlier: 3.540A pdb=" N LEU B 113 " --> pdb=" O PRO B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 161 removed outlier: 4.324A pdb=" N ASP B 128 " --> pdb=" O ARG B 124 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER B 129 " --> pdb=" O VAL B 125 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N PHE B 144 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N VAL B 145 " --> pdb=" O ASN B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 209 Proline residue: B 173 - end of helix Processing helix chain 'B' and resid 212 through 218 Processing helix chain 'B' and resid 219 through 247 removed outlier: 3.830A pdb=" N MET B 223 " --> pdb=" O ALA B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 273 Processing helix chain 'B' and resid 278 through 321 removed outlier: 4.443A pdb=" N THR B 290 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLN B 291 " --> pdb=" O ASN B 287 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LYS B 294 " --> pdb=" O THR B 290 " (cutoff:3.500A) Proline residue: B 295 - end of helix removed outlier: 4.646A pdb=" N SER B 304 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N GLU B 305 " --> pdb=" O SER B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 389 Processing helix chain 'B' and resid 410 through 417 Processing helix chain 'B' and resid 431 through 437 Processing helix chain 'B' and resid 444 through 455 Processing helix chain 'B' and resid 457 through 464 Processing helix chain 'B' and resid 466 through 470 Processing helix chain 'B' and resid 472 through 477 Processing helix chain 'B' and resid 480 through 495 removed outlier: 4.116A pdb=" N ASN B 495 " --> pdb=" O ARG B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 525 Processing helix chain 'B' and resid 536 through 542 Processing helix chain 'B' and resid 559 through 567 Processing helix chain 'B' and resid 568 through 576 Processing sheet with id=AA1, first strand: chain 'A' and resid 350 through 358 removed outlier: 5.719A pdb=" N GLN A 351 " --> pdb=" O PHE A 340 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N PHE A 340 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N PHE A 355 " --> pdb=" O ASP A 336 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N ASP A 336 " --> pdb=" O PHE A 355 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N THR A 357 " --> pdb=" O GLU A 334 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N GLU A 334 " --> pdb=" O THR A 357 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N LYS A 337 " --> pdb=" O SER A 390 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N SER A 390 " --> pdb=" O LYS A 337 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 410 through 413 removed outlier: 6.480A pdb=" N ALA A 411 " --> pdb=" O ILE A 494 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ASP A 496 " --> pdb=" O ALA A 411 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL A 413 " --> pdb=" O ASP A 496 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N LEU A 493 " --> pdb=" O ILE A 524 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ILE A 526 " --> pdb=" O LEU A 493 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU A 495 " --> pdb=" O ILE A 526 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N LEU A 363 " --> pdb=" O ILE A 525 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N SER A 362 " --> pdb=" O GLN A 538 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N LEU A 540 " --> pdb=" O SER A 362 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N GLY A 364 " --> pdb=" O LEU A 540 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N LEU A 542 " --> pdb=" O GLY A 364 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 422 through 423 removed outlier: 3.529A pdb=" N GLY A 422 " --> pdb=" O VAL A 465 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 358 through 364 removed outlier: 4.484A pdb=" N ASP B 360 " --> pdb=" O VAL B 347 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL B 347 " --> pdb=" O ASP B 360 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N SER B 362 " --> pdb=" O ASP B 345 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ASP B 345 " --> pdb=" O SER B 362 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ASP B 364 " --> pdb=" O GLN B 343 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLN B 343 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N PHE B 344 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU B 400 " --> pdb=" O PHE B 344 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N HIS B 346 " --> pdb=" O GLN B 398 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N GLN B 398 " --> pdb=" O HIS B 346 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 418 through 420 removed outlier: 6.564A pdb=" N LEU B 500 " --> pdb=" O PHE B 531 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ILE B 533 " --> pdb=" O LEU B 500 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N LEU B 502 " --> pdb=" O ILE B 533 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ALA B 372 " --> pdb=" O LEU B 547 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N MET B 549 " --> pdb=" O ALA B 372 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU B 556 " --> pdb=" O VAL B 548 " (cutoff:3.500A) 623 hydrogen bonds defined for protein. 1830 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: 1.48 Time building geometry restraints manager: 0.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2920 1.34 - 1.46: 1271 1.46 - 1.57: 4932 1.57 - 1.69: 0 1.69 - 1.81: 77 Bond restraints: 9200 Sorted by residual: bond pdb=" CA ILE A 526 " pdb=" CB ILE A 526 " ideal model delta sigma weight residual 1.540 1.529 0.011 1.36e-02 5.41e+03 6.90e-01 bond pdb=" CB ILE A 139 " pdb=" CG2 ILE A 139 " ideal model delta sigma weight residual 1.521 1.494 0.027 3.30e-02 9.18e+02 6.58e-01 bond pdb=" C VAL B 302 " pdb=" O VAL B 302 " ideal model delta sigma weight residual 1.242 1.233 0.009 1.13e-02 7.83e+03 6.00e-01 bond pdb=" CB ILE B 489 " pdb=" CG2 ILE B 489 " ideal model delta sigma weight residual 1.521 1.497 0.024 3.30e-02 9.18e+02 5.29e-01 bond pdb=" CB ASP B 510 " pdb=" CG ASP B 510 " ideal model delta sigma weight residual 1.516 1.534 -0.018 2.50e-02 1.60e+03 5.29e-01 ... (remaining 9195 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 12221 1.42 - 2.83: 188 2.83 - 4.25: 37 4.25 - 5.66: 13 5.66 - 7.08: 2 Bond angle restraints: 12461 Sorted by residual: angle pdb=" N PHE A 134 " pdb=" CA PHE A 134 " pdb=" C PHE A 134 " ideal model delta sigma weight residual 113.18 108.23 4.95 1.33e+00 5.65e-01 1.38e+01 angle pdb=" CA PHE A 134 " pdb=" C PHE A 134 " pdb=" N LEU A 135 " ideal model delta sigma weight residual 118.22 115.47 2.75 1.03e+00 9.43e-01 7.11e+00 angle pdb=" CG1 ILE B 373 " pdb=" CB ILE B 373 " pdb=" CG2 ILE B 373 " ideal model delta sigma weight residual 110.70 103.62 7.08 3.00e+00 1.11e-01 5.57e+00 angle pdb=" N GLN B 339 " pdb=" CA GLN B 339 " pdb=" C GLN B 339 " ideal model delta sigma weight residual 113.18 110.21 2.97 1.33e+00 5.65e-01 4.98e+00 angle pdb=" CA GLN B 353 " pdb=" CB GLN B 353 " pdb=" CG GLN B 353 " ideal model delta sigma weight residual 114.10 118.43 -4.33 2.00e+00 2.50e-01 4.68e+00 ... (remaining 12456 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.57: 5026 15.57 - 31.15: 421 31.15 - 46.72: 93 46.72 - 62.29: 11 62.29 - 77.86: 8 Dihedral angle restraints: 5559 sinusoidal: 2228 harmonic: 3331 Sorted by residual: dihedral pdb=" CA ASN A 382 " pdb=" C ASN A 382 " pdb=" N LEU A 383 " pdb=" CA LEU A 383 " ideal model delta harmonic sigma weight residual 180.00 162.08 17.92 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA ILE B 533 " pdb=" C ILE B 533 " pdb=" N ALA B 534 " pdb=" CA ALA B 534 " ideal model delta harmonic sigma weight residual -180.00 -163.03 -16.97 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA ILE A 380 " pdb=" C ILE A 380 " pdb=" N MET A 381 " pdb=" CA MET A 381 " ideal model delta harmonic sigma weight residual 180.00 164.60 15.40 0 5.00e+00 4.00e-02 9.48e+00 ... (remaining 5556 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1083 0.039 - 0.078: 317 0.078 - 0.117: 66 0.117 - 0.155: 6 0.155 - 0.194: 1 Chirality restraints: 1473 Sorted by residual: chirality pdb=" CB ILE B 373 " pdb=" CA ILE B 373 " pdb=" CG1 ILE B 373 " pdb=" CG2 ILE B 373 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.19 2.00e-01 2.50e+01 9.44e-01 chirality pdb=" CA ILE B 533 " pdb=" N ILE B 533 " pdb=" C ILE B 533 " pdb=" CB ILE B 533 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.14e-01 chirality pdb=" CA ILE B 325 " pdb=" N ILE B 325 " pdb=" C ILE B 325 " pdb=" CB ILE B 325 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.99e-01 ... (remaining 1470 not shown) Planarity restraints: 1570 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 18 " -0.021 5.00e-02 4.00e+02 3.22e-02 1.66e+00 pdb=" N PRO A 19 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 19 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 19 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 294 " -0.020 5.00e-02 4.00e+02 3.03e-02 1.47e+00 pdb=" N PRO B 295 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO B 295 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 295 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 135 " 0.006 2.00e-02 2.50e+03 1.15e-02 1.32e+00 pdb=" C LEU A 135 " -0.020 2.00e-02 2.50e+03 pdb=" O LEU A 135 " 0.007 2.00e-02 2.50e+03 pdb=" N ARG A 136 " 0.007 2.00e-02 2.50e+03 ... (remaining 1567 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 294 2.72 - 3.27: 9835 3.27 - 3.81: 15636 3.81 - 4.36: 17922 4.36 - 4.90: 31409 Nonbonded interactions: 75096 Sorted by model distance: nonbonded pdb=" O GLU B 206 " pdb=" OG1 THR B 209 " model vdw 2.176 3.040 nonbonded pdb=" OG1 THR B 31 " pdb=" OH TYR B 86 " model vdw 2.281 3.040 nonbonded pdb=" NH2 ARG A 515 " pdb=" OD2 ASP A 537 " model vdw 2.295 3.120 nonbonded pdb=" OD2 ASP B 16 " pdb=" OH TYR B 317 " model vdw 2.301 3.040 nonbonded pdb=" NH1 ARG B 12 " pdb=" OD1 ASP B 321 " model vdw 2.340 3.120 ... (remaining 75091 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=1.00 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: 1.840 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: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.700 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 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 0.030 9200 Z= 0.133 Angle : 0.484 7.079 12461 Z= 0.256 Chirality : 0.038 0.194 1473 Planarity : 0.003 0.034 1570 Dihedral : 12.291 77.864 3405 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % 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 are not related in a simple way. whole: 2.17 (0.26), residues: 1138 helix: 2.44 (0.18), residues: 790 sheet: -1.77 (0.74), residues: 54 loop : -0.75 (0.37), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 136 TYR 0.014 0.001 TYR A 181 PHE 0.014 0.001 PHE B 493 TRP 0.014 0.001 TRP A 228 HIS 0.004 0.001 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 9200) covalent geometry : angle 0.48398 / 0.26 (12461) hydrogen bonds : bond 0.13039 / 9.01 ( 623) hydrogen bonds : angle 4.60636 / 3.48 ( 1830) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 LYS cc_start: 0.7851 (mmmt) cc_final: 0.7563 (mtpt) REVERT: A 223 LYS cc_start: 0.8251 (mtmt) cc_final: 0.7870 (mttm) REVERT: A 271 MET cc_start: 0.8382 (mmt) cc_final: 0.8162 (mmt) REVERT: A 402 ASN cc_start: 0.7936 (p0) cc_final: 0.7352 (p0) REVERT: A 404 LYS cc_start: 0.8734 (tttp) cc_final: 0.8375 (ttpp) REVERT: A 424 ILE cc_start: 0.8286 (mm) cc_final: 0.7941 (mm) REVERT: A 446 ASP cc_start: 0.8525 (t70) cc_final: 0.8320 (t70) REVERT: A 470 ARG cc_start: 0.8170 (ptm-80) cc_final: 0.7602 (tmm160) REVERT: A 488 ARG cc_start: 0.7897 (ttp80) cc_final: 0.7483 (ttm110) REVERT: A 544 LYS cc_start: 0.7868 (mtmm) cc_final: 0.7347 (mmmt) REVERT: B 21 CYS cc_start: 0.7219 (t) cc_final: 0.6905 (p) REVERT: B 80 TRP cc_start: 0.8895 (t60) cc_final: 0.8492 (t60) REVERT: B 96 SER cc_start: 0.8102 (m) cc_final: 0.7762 (p) REVERT: B 159 ARG cc_start: 0.6897 (tmm160) cc_final: 0.6028 (ttp80) REVERT: B 184 ARG cc_start: 0.6862 (mtm180) cc_final: 0.6550 (ptt90) REVERT: B 323 ASP cc_start: 0.7745 (p0) cc_final: 0.7334 (m-30) REVERT: B 345 ASP cc_start: 0.8407 (t0) cc_final: 0.7700 (m-30) REVERT: B 459 PHE cc_start: 0.6709 (m-80) cc_final: 0.6300 (m-10) REVERT: B 525 MET cc_start: 0.7725 (mtm) cc_final: 0.7224 (mtm) REVERT: B 542 ASN cc_start: 0.8677 (m-40) cc_final: 0.8244 (m-40) REVERT: B 556 GLU cc_start: 0.7073 (mm-30) cc_final: 0.6863 (mm-30) REVERT: B 571 TYR cc_start: 0.8637 (t80) cc_final: 0.8006 (t80) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.1106 time to fit residues: 28.5208 Evaluate side-chains 136 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 0.3980 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 397 GLN ** A 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.134369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.103050 restraints weight = 12721.541| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.11 r_work: 0.3085 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9200 Z= 0.224 Angle : 0.577 7.399 12461 Z= 0.294 Chirality : 0.042 0.206 1473 Planarity : 0.004 0.038 1570 Dihedral : 3.774 18.600 1233 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.61 % Allowed : 6.04 % Favored : 92.35 % 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 are not related in a simple way. whole: 1.72 (0.25), residues: 1138 helix: 2.03 (0.18), residues: 799 sheet: -2.18 (0.70), residues: 54 loop : -0.72 (0.38), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 305 TYR 0.015 0.001 TYR A 568 PHE 0.016 0.001 PHE A 244 TRP 0.007 0.001 TRP A 442 HIS 0.005 0.001 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00539 / 0.22 ( 9200) covalent geometry : angle 0.57704 / 0.29 (12461) hydrogen bonds : bond 0.04738 / 3.09 ( 623) hydrogen bonds : angle 4.12939 / 3.07 ( 1830) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 134 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 LYS cc_start: 0.8192 (mmmt) cc_final: 0.7842 (mtpt) REVERT: A 223 LYS cc_start: 0.8892 (mtmt) cc_final: 0.8638 (mttp) REVERT: A 328 GLN cc_start: 0.8811 (tt0) cc_final: 0.8383 (tt0) REVERT: A 334 GLU cc_start: 0.7807 (tm-30) cc_final: 0.7509 (tp30) REVERT: A 388 PHE cc_start: 0.7041 (m-80) cc_final: 0.6698 (m-80) REVERT: A 404 LYS cc_start: 0.8830 (tttp) cc_final: 0.8418 (ttpp) REVERT: A 447 MET cc_start: 0.8339 (mtm) cc_final: 0.8033 (mtp) REVERT: A 488 ARG cc_start: 0.8087 (ttp80) cc_final: 0.7606 (ttm110) REVERT: A 518 LEU cc_start: 0.9022 (mm) cc_final: 0.8805 (mm) REVERT: A 544 LYS cc_start: 0.8414 (mtmm) cc_final: 0.7940 (mmmt) REVERT: B 159 ARG cc_start: 0.7559 (tmm160) cc_final: 0.6736 (ttp80) REVERT: B 184 ARG cc_start: 0.7222 (mtm180) cc_final: 0.6793 (mtm110) REVERT: B 306 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8411 (mp) REVERT: B 323 ASP cc_start: 0.8276 (p0) cc_final: 0.7863 (m-30) REVERT: B 345 ASP cc_start: 0.8802 (t0) cc_final: 0.8170 (m-30) REVERT: B 542 ASN cc_start: 0.8590 (m-40) cc_final: 0.8210 (m-40) outliers start: 16 outliers final: 11 residues processed: 142 average time/residue: 0.0951 time to fit residues: 18.8333 Evaluate side-chains 126 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain A residue 527 SER Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 472 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 18 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 chunk 107 optimal weight: 0.7980 chunk 71 optimal weight: 0.5980 chunk 87 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 88 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 443 HIS B 82 ASN ** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.133709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.102353 restraints weight = 12415.033| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.12 r_work: 0.3084 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9200 Z= 0.144 Angle : 0.501 9.649 12461 Z= 0.253 Chirality : 0.039 0.140 1473 Planarity : 0.003 0.036 1570 Dihedral : 3.742 18.831 1233 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.81 % Allowed : 9.87 % Favored : 88.32 % 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 are not related in a simple way. whole: 1.76 (0.25), residues: 1138 helix: 2.06 (0.18), residues: 800 sheet: -2.30 (0.68), residues: 54 loop : -0.69 (0.38), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 305 TYR 0.013 0.001 TYR B 112 PHE 0.014 0.001 PHE A 453 TRP 0.010 0.001 TRP A 406 HIS 0.003 0.001 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 9200) covalent geometry : angle 0.50059 / 0.25 (12461) hydrogen bonds : bond 0.04275 / 2.78 ( 623) hydrogen bonds : angle 3.97631 / 2.93 ( 1830) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 LYS cc_start: 0.8080 (mmmt) cc_final: 0.7782 (mtpt) REVERT: A 223 LYS cc_start: 0.8906 (mtmt) cc_final: 0.8638 (mttp) REVERT: A 328 GLN cc_start: 0.8770 (tt0) cc_final: 0.8353 (tt0) REVERT: A 334 GLU cc_start: 0.7820 (tm-30) cc_final: 0.6850 (tm-30) REVERT: A 388 PHE cc_start: 0.6989 (m-80) cc_final: 0.6597 (m-80) REVERT: A 404 LYS cc_start: 0.8780 (tttp) cc_final: 0.8345 (ttpp) REVERT: A 447 MET cc_start: 0.8216 (mtm) cc_final: 0.7925 (mtp) REVERT: A 453 PHE cc_start: 0.7133 (m-10) cc_final: 0.6578 (m-10) REVERT: A 488 ARG cc_start: 0.8083 (ttp80) cc_final: 0.7595 (ttm110) REVERT: A 518 LEU cc_start: 0.9046 (mm) cc_final: 0.8810 (mm) REVERT: A 544 LYS cc_start: 0.8379 (mtmm) cc_final: 0.7868 (mmmt) REVERT: B 159 ARG cc_start: 0.7630 (tmm160) cc_final: 0.6927 (ttp80) REVERT: B 184 ARG cc_start: 0.7298 (mtm180) cc_final: 0.6981 (ptt90) REVERT: B 345 ASP cc_start: 0.8781 (t0) cc_final: 0.8160 (m-30) REVERT: B 542 ASN cc_start: 0.8552 (m-40) cc_final: 0.8132 (m-40) REVERT: B 549 MET cc_start: 0.8752 (mtp) cc_final: 0.8527 (mtm) REVERT: B 570 TYR cc_start: 0.8522 (t80) cc_final: 0.8000 (t80) outliers start: 18 outliers final: 13 residues processed: 136 average time/residue: 0.0949 time to fit residues: 17.8099 Evaluate side-chains 130 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 117 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 446 ASP Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain A residue 527 SER Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 566 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 18 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 87 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 112 optimal weight: 0.8980 chunk 31 optimal weight: 6.9990 chunk 4 optimal weight: 0.0040 chunk 15 optimal weight: 0.9980 chunk 41 optimal weight: 0.1980 chunk 104 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.134017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.103452 restraints weight = 12427.421| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.06 r_work: 0.3108 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9200 Z= 0.122 Angle : 0.479 9.617 12461 Z= 0.241 Chirality : 0.038 0.140 1473 Planarity : 0.003 0.035 1570 Dihedral : 3.697 22.402 1233 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.01 % Allowed : 11.28 % Favored : 86.71 % 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 are not related in a simple way. whole: 1.88 (0.25), residues: 1138 helix: 2.14 (0.18), residues: 800 sheet: -2.35 (0.75), residues: 39 loop : -0.72 (0.36), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 305 TYR 0.011 0.001 TYR B 260 PHE 0.011 0.001 PHE A 244 TRP 0.007 0.001 TRP A 442 HIS 0.003 0.001 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 9200) covalent geometry : angle 0.47942 / 0.24 (12461) hydrogen bonds : bond 0.04040 / 2.63 ( 623) hydrogen bonds : angle 3.88318 / 2.86 ( 1830) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: A 103 LYS cc_start: 0.8098 (mmmt) cc_final: 0.7800 (mtpt) REVERT: A 223 LYS cc_start: 0.8910 (mtmt) cc_final: 0.8637 (mttm) REVERT: A 328 GLN cc_start: 0.8771 (tt0) cc_final: 0.8360 (tt0) REVERT: A 334 GLU cc_start: 0.7823 (tm-30) cc_final: 0.6900 (tm-30) REVERT: A 388 PHE cc_start: 0.7057 (m-80) cc_final: 0.6639 (m-80) REVERT: A 404 LYS cc_start: 0.8747 (tttp) cc_final: 0.8356 (ttpp) REVERT: A 447 MET cc_start: 0.8155 (mtm) cc_final: 0.7714 (mtp) REVERT: A 449 GLN cc_start: 0.8814 (mp10) cc_final: 0.8106 (mp10) REVERT: A 488 ARG cc_start: 0.8030 (ttp80) cc_final: 0.7570 (ttm110) REVERT: A 518 LEU cc_start: 0.9107 (mm) cc_final: 0.8904 (mm) REVERT: A 544 LYS cc_start: 0.8342 (mtmm) cc_final: 0.7828 (mmmt) REVERT: B 159 ARG cc_start: 0.7614 (tmm160) cc_final: 0.6912 (ttp80) REVERT: B 184 ARG cc_start: 0.7284 (mtm180) cc_final: 0.6986 (ptt90) REVERT: B 345 ASP cc_start: 0.8784 (t0) cc_final: 0.8190 (m-30) REVERT: B 542 ASN cc_start: 0.8459 (m-40) cc_final: 0.8046 (m-40) REVERT: B 549 MET cc_start: 0.8707 (mtp) cc_final: 0.8478 (mtm) REVERT: B 570 TYR cc_start: 0.8513 (t80) cc_final: 0.8000 (t80) outliers start: 20 outliers final: 12 residues processed: 134 average time/residue: 0.0987 time to fit residues: 17.9749 Evaluate side-chains 127 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 446 ASP Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 566 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 15 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 102 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 295 ASN ** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.135679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.104847 restraints weight = 12651.109| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.06 r_work: 0.3115 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9200 Z= 0.143 Angle : 0.482 9.674 12461 Z= 0.244 Chirality : 0.038 0.138 1473 Planarity : 0.003 0.036 1570 Dihedral : 3.649 19.356 1233 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.32 % Allowed : 11.88 % Favored : 85.80 % 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 are not related in a simple way. whole: 1.89 (0.25), residues: 1138 helix: 2.15 (0.18), residues: 800 sheet: -2.37 (0.75), residues: 39 loop : -0.70 (0.36), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 421 TYR 0.010 0.001 TYR B 112 PHE 0.012 0.001 PHE A 244 TRP 0.005 0.001 TRP A 442 HIS 0.003 0.001 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 ( 9200) covalent geometry : angle 0.48240 / 0.24 (12461) hydrogen bonds : bond 0.04075 / 2.66 ( 623) hydrogen bonds : angle 3.87243 / 2.85 ( 1830) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 LYS cc_start: 0.8198 (mmmt) cc_final: 0.7882 (mtpt) REVERT: A 223 LYS cc_start: 0.8924 (mtmt) cc_final: 0.8642 (mttp) REVERT: A 328 GLN cc_start: 0.8764 (tt0) cc_final: 0.8363 (tt0) REVERT: A 334 GLU cc_start: 0.7810 (tm-30) cc_final: 0.6923 (tm-30) REVERT: A 404 LYS cc_start: 0.8661 (tttp) cc_final: 0.8268 (ttpp) REVERT: A 447 MET cc_start: 0.8232 (mtm) cc_final: 0.7687 (mtp) REVERT: A 449 GLN cc_start: 0.8724 (mp10) cc_final: 0.8039 (mp10) REVERT: A 488 ARG cc_start: 0.8035 (ttp80) cc_final: 0.7591 (ttm110) REVERT: A 518 LEU cc_start: 0.9062 (mm) cc_final: 0.8857 (mm) REVERT: A 544 LYS cc_start: 0.8409 (mtmm) cc_final: 0.7884 (mmmt) REVERT: B 159 ARG cc_start: 0.7651 (tmm160) cc_final: 0.6963 (ttp80) REVERT: B 345 ASP cc_start: 0.8800 (t0) cc_final: 0.8209 (m-30) REVERT: B 542 ASN cc_start: 0.8419 (m-40) cc_final: 0.7984 (m-40) REVERT: B 570 TYR cc_start: 0.8559 (t80) cc_final: 0.8149 (t80) outliers start: 23 outliers final: 17 residues processed: 137 average time/residue: 0.0950 time to fit residues: 18.4020 Evaluate side-chains 130 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 446 ASP Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain A residue 527 SER Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 566 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 42 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 52 optimal weight: 0.5980 chunk 88 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.134126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.103160 restraints weight = 12443.678| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.08 r_work: 0.3097 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9200 Z= 0.139 Angle : 0.481 9.397 12461 Z= 0.242 Chirality : 0.038 0.138 1473 Planarity : 0.003 0.036 1570 Dihedral : 3.636 19.416 1233 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.01 % Allowed : 13.19 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.97 (0.25), residues: 1138 helix: 2.20 (0.18), residues: 800 sheet: -1.91 (0.98), residues: 28 loop : -0.78 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 421 TYR 0.008 0.001 TYR B 86 PHE 0.012 0.001 PHE A 244 TRP 0.005 0.001 TRP A 256 HIS 0.003 0.001 HIS B 433 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 9200) covalent geometry : angle 0.48114 / 0.24 (12461) hydrogen bonds : bond 0.04034 / 2.64 ( 623) hydrogen bonds : angle 3.85824 / 2.83 ( 1830) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: A 103 LYS cc_start: 0.8132 (mmmt) cc_final: 0.7818 (mtpt) REVERT: A 223 LYS cc_start: 0.8920 (mtmt) cc_final: 0.8630 (mttp) REVERT: A 328 GLN cc_start: 0.8742 (tt0) cc_final: 0.8335 (tt0) REVERT: A 334 GLU cc_start: 0.7759 (tm-30) cc_final: 0.6888 (tm-30) REVERT: A 388 PHE cc_start: 0.7130 (m-10) cc_final: 0.6703 (m-80) REVERT: A 404 LYS cc_start: 0.8606 (tttp) cc_final: 0.8261 (ttpp) REVERT: A 447 MET cc_start: 0.8246 (mtm) cc_final: 0.7833 (mtp) REVERT: A 449 GLN cc_start: 0.8662 (mp10) cc_final: 0.8091 (mp10) REVERT: A 488 ARG cc_start: 0.8031 (ttp80) cc_final: 0.7585 (ttm110) REVERT: A 544 LYS cc_start: 0.8357 (mtmm) cc_final: 0.7827 (mmmt) REVERT: B 159 ARG cc_start: 0.7639 (tmm160) cc_final: 0.6931 (ttp80) REVERT: B 345 ASP cc_start: 0.8774 (t0) cc_final: 0.8199 (m-30) REVERT: B 570 TYR cc_start: 0.8562 (t80) cc_final: 0.8055 (t80) REVERT: B 574 GLN cc_start: 0.8170 (mm-40) cc_final: 0.7928 (mm110) outliers start: 20 outliers final: 16 residues processed: 136 average time/residue: 0.0981 time to fit residues: 18.7706 Evaluate side-chains 129 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 446 ASP Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain A residue 527 SER Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 566 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 111 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 83 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 104 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.132355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.101971 restraints weight = 12424.534| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.04 r_work: 0.3092 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9200 Z= 0.147 Angle : 0.490 9.291 12461 Z= 0.245 Chirality : 0.038 0.158 1473 Planarity : 0.003 0.036 1570 Dihedral : 3.623 19.172 1233 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.01 % Allowed : 13.90 % Favored : 84.09 % 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 are not related in a simple way. whole: 1.99 (0.25), residues: 1138 helix: 2.21 (0.18), residues: 800 sheet: -1.88 (0.99), residues: 28 loop : -0.76 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 421 TYR 0.009 0.001 TYR B 86 PHE 0.013 0.001 PHE A 244 TRP 0.005 0.001 TRP A 256 HIS 0.003 0.001 HIS B 433 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 ( 9200) covalent geometry : angle 0.48996 / 0.25 (12461) hydrogen bonds : bond 0.04095 / 2.66 ( 623) hydrogen bonds : angle 3.86825 / 2.84 ( 1830) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.390 Fit side-chains revert: symmetry clash REVERT: A 103 LYS cc_start: 0.8124 (mmmt) cc_final: 0.7787 (mtpt) REVERT: A 223 LYS cc_start: 0.8870 (mtmt) cc_final: 0.8544 (mttm) REVERT: A 334 GLU cc_start: 0.7769 (tm-30) cc_final: 0.6906 (tm-30) REVERT: A 388 PHE cc_start: 0.7128 (m-10) cc_final: 0.6682 (m-80) REVERT: A 404 LYS cc_start: 0.8647 (tttp) cc_final: 0.8288 (ttpp) REVERT: A 447 MET cc_start: 0.8239 (mtm) cc_final: 0.7833 (mtp) REVERT: A 449 GLN cc_start: 0.8616 (mp10) cc_final: 0.8070 (mp10) REVERT: A 488 ARG cc_start: 0.8036 (ttp80) cc_final: 0.7567 (ttm110) REVERT: A 544 LYS cc_start: 0.8358 (mtmm) cc_final: 0.7807 (mmmt) REVERT: B 159 ARG cc_start: 0.7583 (tmm160) cc_final: 0.6887 (ttp80) REVERT: B 570 TYR cc_start: 0.8585 (t80) cc_final: 0.8137 (t80) REVERT: B 574 GLN cc_start: 0.8170 (mm-40) cc_final: 0.7935 (mm110) outliers start: 20 outliers final: 17 residues processed: 128 average time/residue: 0.0938 time to fit residues: 16.8650 Evaluate side-chains 127 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 446 ASP Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain A residue 527 SER Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 566 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 112 optimal weight: 0.7980 chunk 99 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 46 optimal weight: 0.1980 chunk 111 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 104 optimal weight: 0.0980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.137098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.106569 restraints weight = 12594.528| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.06 r_work: 0.3142 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9200 Z= 0.115 Angle : 0.477 9.199 12461 Z= 0.237 Chirality : 0.038 0.162 1473 Planarity : 0.003 0.036 1570 Dihedral : 3.590 19.426 1233 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.22 % Allowed : 13.80 % Favored : 83.99 % 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 are not related in a simple way. whole: 2.12 (0.25), residues: 1138 helix: 2.31 (0.18), residues: 800 sheet: -0.85 (1.29), residues: 18 loop : -0.86 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 421 TYR 0.008 0.001 TYR B 86 PHE 0.013 0.001 PHE A 244 TRP 0.007 0.001 TRP A 228 HIS 0.003 0.001 HIS A 567 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 ( 9200) covalent geometry : angle 0.47723 / 0.24 (12461) hydrogen bonds : bond 0.03926 / 2.55 ( 623) hydrogen bonds : angle 3.79682 / 2.78 ( 1830) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 LYS cc_start: 0.8185 (mmmt) cc_final: 0.7865 (mtpt) REVERT: A 223 LYS cc_start: 0.8871 (mtmt) cc_final: 0.8553 (mttm) REVERT: A 334 GLU cc_start: 0.7751 (tm-30) cc_final: 0.6921 (tm-30) REVERT: A 388 PHE cc_start: 0.7170 (m-10) cc_final: 0.6729 (m-80) REVERT: A 404 LYS cc_start: 0.8627 (tttp) cc_final: 0.8284 (ttpp) REVERT: A 428 LEU cc_start: 0.8568 (mp) cc_final: 0.8361 (mp) REVERT: A 447 MET cc_start: 0.8249 (mtm) cc_final: 0.7706 (mtp) REVERT: A 449 GLN cc_start: 0.8563 (mp10) cc_final: 0.8082 (mp10) REVERT: A 488 ARG cc_start: 0.8006 (ttp80) cc_final: 0.7562 (ttm110) REVERT: A 544 LYS cc_start: 0.8351 (mtmm) cc_final: 0.7807 (mmmt) REVERT: B 159 ARG cc_start: 0.7633 (tmm160) cc_final: 0.6913 (ttp80) REVERT: B 563 LEU cc_start: 0.8431 (mm) cc_final: 0.8161 (mm) REVERT: B 570 TYR cc_start: 0.8530 (t80) cc_final: 0.8057 (t80) REVERT: B 574 GLN cc_start: 0.8162 (mm-40) cc_final: 0.7931 (mm110) outliers start: 22 outliers final: 16 residues processed: 134 average time/residue: 0.0916 time to fit residues: 17.2539 Evaluate side-chains 132 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 446 ASP Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain A residue 527 SER Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 472 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 74 optimal weight: 2.9990 chunk 102 optimal weight: 0.0370 chunk 93 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 24 optimal weight: 0.0980 chunk 92 optimal weight: 0.7980 chunk 85 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.134993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.105511 restraints weight = 12433.935| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.99 r_work: 0.3154 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9200 Z= 0.117 Angle : 0.484 9.003 12461 Z= 0.240 Chirality : 0.038 0.210 1473 Planarity : 0.003 0.036 1570 Dihedral : 3.607 18.692 1233 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.22 % Allowed : 14.00 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.12 (0.25), residues: 1138 helix: 2.32 (0.18), residues: 800 sheet: -0.92 (1.28), residues: 18 loop : -0.87 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 421 TYR 0.010 0.001 TYR B 86 PHE 0.012 0.001 PHE A 244 TRP 0.011 0.001 TRP A 228 HIS 0.003 0.001 HIS A 567 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 ( 9200) covalent geometry : angle 0.48422 / 0.24 (12461) hydrogen bonds : bond 0.03893 / 2.54 ( 623) hydrogen bonds : angle 3.76560 / 2.76 ( 1830) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 LYS cc_start: 0.8172 (mmmt) cc_final: 0.7853 (mtpt) REVERT: A 223 LYS cc_start: 0.8867 (mtmt) cc_final: 0.8543 (mttm) REVERT: A 334 GLU cc_start: 0.7721 (tm-30) cc_final: 0.6860 (tm-30) REVERT: A 388 PHE cc_start: 0.7171 (m-10) cc_final: 0.6944 (m-80) REVERT: A 404 LYS cc_start: 0.8620 (tttp) cc_final: 0.8279 (ttpp) REVERT: A 428 LEU cc_start: 0.8591 (mp) cc_final: 0.8385 (mp) REVERT: A 447 MET cc_start: 0.8065 (mtm) cc_final: 0.7618 (mtp) REVERT: A 449 GLN cc_start: 0.8576 (mp10) cc_final: 0.8090 (mp10) REVERT: A 488 ARG cc_start: 0.7977 (ttp80) cc_final: 0.7551 (ttm110) REVERT: A 544 LYS cc_start: 0.8337 (mtmm) cc_final: 0.7794 (mmmt) REVERT: B 159 ARG cc_start: 0.7603 (tmm160) cc_final: 0.6884 (ttp80) REVERT: B 563 LEU cc_start: 0.8415 (mm) cc_final: 0.8152 (mm) REVERT: B 570 TYR cc_start: 0.8543 (t80) cc_final: 0.8072 (t80) REVERT: B 574 GLN cc_start: 0.8151 (mm-40) cc_final: 0.7923 (mm110) outliers start: 22 outliers final: 19 residues processed: 131 average time/residue: 0.0900 time to fit residues: 16.7069 Evaluate side-chains 134 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 434 TYR Chi-restraints excluded: chain A residue 446 ASP Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain A residue 527 SER Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 472 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 23 optimal weight: 0.0980 chunk 11 optimal weight: 0.6980 chunk 85 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 546 HIS ** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.134346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.104933 restraints weight = 12368.961| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.98 r_work: 0.3138 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9200 Z= 0.130 Angle : 0.490 8.772 12461 Z= 0.244 Chirality : 0.038 0.205 1473 Planarity : 0.003 0.036 1570 Dihedral : 3.614 18.557 1233 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.32 % Allowed : 14.30 % Favored : 83.38 % 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 are not related in a simple way. whole: 2.12 (0.25), residues: 1138 helix: 2.30 (0.18), residues: 800 sheet: -0.79 (1.30), residues: 18 loop : -0.85 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 421 TYR 0.010 0.001 TYR B 260 PHE 0.012 0.001 PHE B 285 TRP 0.014 0.001 TRP A 228 HIS 0.003 0.001 HIS A 567 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 9200) covalent geometry : angle 0.49012 / 0.24 (12461) hydrogen bonds : bond 0.03941 / 2.57 ( 623) hydrogen bonds : angle 3.77744 / 2.77 ( 1830) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.345 Fit side-chains revert: symmetry clash REVERT: A 9 LYS cc_start: 0.7275 (mmtt) cc_final: 0.7013 (mmtm) REVERT: A 103 LYS cc_start: 0.8203 (mmmt) cc_final: 0.7870 (mtpt) REVERT: A 223 LYS cc_start: 0.8890 (mtmt) cc_final: 0.8565 (mttp) REVERT: A 334 GLU cc_start: 0.7659 (tm-30) cc_final: 0.6901 (tm-30) REVERT: A 388 PHE cc_start: 0.7166 (m-10) cc_final: 0.6926 (m-80) REVERT: A 404 LYS cc_start: 0.8619 (tttp) cc_final: 0.8283 (ttpp) REVERT: A 428 LEU cc_start: 0.8504 (mp) cc_final: 0.8275 (mp) REVERT: A 447 MET cc_start: 0.8063 (mtm) cc_final: 0.7592 (mtp) REVERT: A 449 GLN cc_start: 0.8604 (mp10) cc_final: 0.8110 (mp10) REVERT: A 488 ARG cc_start: 0.7942 (ttp80) cc_final: 0.7645 (ttm110) REVERT: A 544 LYS cc_start: 0.8386 (mtmm) cc_final: 0.7852 (mmmt) REVERT: B 159 ARG cc_start: 0.7608 (tmm160) cc_final: 0.6882 (ttp80) REVERT: B 563 LEU cc_start: 0.8415 (mm) cc_final: 0.8161 (mm) REVERT: B 570 TYR cc_start: 0.8584 (t80) cc_final: 0.8338 (t80) outliers start: 23 outliers final: 20 residues processed: 126 average time/residue: 0.0933 time to fit residues: 16.6652 Evaluate side-chains 129 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 434 TYR Chi-restraints excluded: chain A residue 446 ASP Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain A residue 527 SER Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 472 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 107 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 66 optimal weight: 0.3980 chunk 93 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 546 HIS ** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.134881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.105644 restraints weight = 12475.920| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.92 r_work: 0.3147 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9200 Z= 0.143 Angle : 0.504 9.931 12461 Z= 0.251 Chirality : 0.039 0.207 1473 Planarity : 0.003 0.036 1570 Dihedral : 3.653 18.660 1233 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.11 % Allowed : 14.60 % Favored : 83.28 % 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 are not related in a simple way. whole: 2.08 (0.25), residues: 1138 helix: 2.28 (0.18), residues: 800 sheet: -1.80 (1.00), residues: 28 loop : -0.75 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 488 TYR 0.022 0.001 TYR B 112 PHE 0.013 0.001 PHE B 285 TRP 0.014 0.001 TRP A 228 HIS 0.003 0.001 HIS A 567 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 ( 9200) covalent geometry : angle 0.50434 / 0.25 (12461) hydrogen bonds : bond 0.04000 / 2.60 ( 623) hydrogen bonds : angle 3.78555 / 2.77 ( 1830) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2112.40 seconds wall clock time: 37 minutes 2.82 seconds (2222.82 seconds total)