Starting phenix.real_space_refine on Thu Jul 2 17:13:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9x4b_66536/07_2026/9x4b_66536.cif Found real_map, /net/cci-nas-00/data/ceres_data/9x4b_66536/07_2026/9x4b_66536.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9x4b_66536/07_2026/9x4b_66536.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9x4b_66536/07_2026/9x4b_66536.map" model { file = "/net/cci-nas-00/data/ceres_data/9x4b_66536/07_2026/9x4b_66536.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9x4b_66536/07_2026/9x4b_66536.cif" } resolution = 2.84 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= 0.043 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 5 5.49 5 Mg 1 5.21 5 S 40 5.16 5 C 5850 2.51 5 N 1533 2.21 5 O 1671 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: 9100 Number of models: 1 Model: "" Number of chains: 4 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} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.04, per 1000 atoms: 0.22 Number of scatterers: 9100 At special positions: 0 Unit cell: (71.208, 100.104, 138.288, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 40 16.00 P 5 15.00 Mg 1 11.99 O 1671 8.00 N 1533 7.00 C 5850 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: 0.90 Conformation dependent library (CDL) restraints added in 323.7 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: 45 helices and 5 sheets defined 72.0% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 2 through 8 removed outlier: 3.885A pdb=" N LEU A 5 " --> pdb=" O LYS A 2 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL A 6 " --> pdb=" O ALA A 3 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR A 7 " --> pdb=" O LEU A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 11 through 47 Proline residue: A 19 - end of helix Proline residue: A 33 - end of helix removed outlier: 4.879A pdb=" N ILE A 44 " --> pdb=" O VAL A 40 " (cutoff:3.500A) Proline residue: A 45 - end of helix Processing helix chain 'A' and resid 48 through 98 Processing helix chain 'A' and resid 100 through 107 Processing helix chain 'A' and resid 108 through 134 removed outlier: 4.171A pdb=" N ASP A 119 " --> pdb=" O ARG A 115 " (cutoff:3.500A) removed outlier: 4.197A 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 152 through 201 removed outlier: 3.923A pdb=" N LEU A 157 " --> pdb=" O PRO A 153 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N TRP A 158 " --> pdb=" O ARG A 154 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE A 159 " --> pdb=" O LEU A 155 " (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: 3.753A pdb=" N GLU A 214 " --> pdb=" O GLN A 210 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE A 235 " --> pdb=" O LYS A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 264 removed outlier: 3.568A pdb=" N VAL A 260 " --> pdb=" O TRP A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 281 Processing helix chain 'A' and resid 281 through 311 removed outlier: 4.243A pdb=" N GLU A 285 " --> pdb=" O GLN A 281 " (cutoff:3.500A) 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 457 removed outlier: 3.650A pdb=" N VAL A 454 " --> pdb=" O ALA A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 462 Processing helix chain 'A' and resid 473 through 487 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 571 Processing helix chain 'B' and resid 9 through 19 Processing helix chain 'B' and resid 20 through 52 Proline residue: B 42 - end of helix Processing helix chain 'B' and resid 56 through 108 Proline residue: B 83 - end of helix Processing helix chain 'B' and resid 109 through 117 removed outlier: 3.540A pdb=" N LEU B 113 " --> pdb=" O PRO B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 142 removed outlier: 3.934A pdb=" N ASP B 128 " --> pdb=" O ARG B 124 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER B 129 " --> pdb=" O VAL B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 161 Processing helix chain 'B' and resid 161 through 210 Proline residue: B 173 - end of helix Processing helix chain 'B' and resid 210 through 217 Processing helix chain 'B' and resid 219 through 247 removed outlier: 3.595A pdb=" N LYS B 233 " --> pdb=" O GLU B 229 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY B 240 " --> pdb=" O ASN B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 273 Processing helix chain 'B' and resid 278 through 321 removed outlier: 3.603A pdb=" N VAL B 289 " --> pdb=" O PHE B 285 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N THR B 290 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLN B 291 " --> pdb=" O ASN B 287 " (cutoff:3.500A) Proline residue: B 295 - end of helix removed outlier: 4.599A pdb=" N SER B 304 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N GLU B 305 " --> pdb=" O SER B 301 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ILE B 319 " --> pdb=" O ARG B 315 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU B 320 " --> pdb=" O LEU B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 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 463 removed outlier: 3.785A pdb=" N ILE B 461 " --> pdb=" O ALA B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 470 Processing helix chain 'B' and resid 480 through 495 removed outlier: 3.610A pdb=" N ILE B 492 " --> pdb=" O THR B 488 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASN B 495 " --> pdb=" O ARG B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 509 Processing helix chain 'B' and resid 513 through 526 removed outlier: 3.812A pdb=" N LYS B 526 " --> pdb=" O ALA B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 543 Processing helix chain 'B' and resid 559 through 566 Processing helix chain 'B' and resid 568 through 577 Processing sheet with id=AA1, first strand: chain 'A' and resid 348 through 358 removed outlier: 6.414A pdb=" N SER A 349 " --> pdb=" O THR A 341 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N THR A 341 " --> pdb=" O SER A 349 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLN A 351 " --> pdb=" O THR A 339 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N THR A 339 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ILE A 353 " --> pdb=" O LYS A 337 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N MET A 338 " --> pdb=" O PHE A 388 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N PHE A 388 " --> pdb=" O MET A 338 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 410 through 413 removed outlier: 6.473A pdb=" N ALA A 411 " --> pdb=" O ILE A 494 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N ASP A 496 " --> pdb=" O ALA A 411 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL A 413 " --> pdb=" O ASP A 496 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LEU A 493 " --> pdb=" O ILE A 524 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ILE A 526 " --> pdb=" O LEU A 493 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU A 495 " --> pdb=" O ILE A 526 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N GLY A 364 " --> pdb=" O LEU A 540 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N LEU A 542 " --> pdb=" O GLY A 364 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE A 366 " --> pdb=" O LEU A 542 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY A 549 " --> pdb=" O VAL A 541 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ASP A 543 " --> pdb=" O GLN A 547 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N GLN A 547 " --> pdb=" O ASP A 543 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 422 through 423 Processing sheet with id=AA4, first strand: chain 'B' and resid 358 through 363 removed outlier: 3.671A pdb=" N ASP B 360 " --> pdb=" O VAL B 347 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N VAL B 347 " --> pdb=" O ASP B 360 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N SER B 362 " --> pdb=" O ASP B 345 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ASP B 345 " --> pdb=" O SER B 362 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL B 347 " --> pdb=" O LYS B 396 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LYS B 396 " --> pdb=" O VAL B 347 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 418 through 420 removed outlier: 6.001A pdb=" N GLY B 419 " --> pdb=" O ILE B 501 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N ASP B 503 " --> pdb=" O GLY B 419 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N MET B 549 " --> pdb=" O VAL B 374 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE B 546 " --> pdb=" O HIS B 557 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N HIS B 557 " --> pdb=" O ILE B 546 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N VAL B 548 " --> pdb=" O VAL B 555 " (cutoff:3.500A) 629 hydrogen bonds defined for protein. 1854 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: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2927 1.34 - 1.46: 1629 1.46 - 1.58: 4621 1.58 - 1.69: 8 1.69 - 1.81: 77 Bond restraints: 9262 Sorted by residual: bond pdb=" CA ASN B 550 " pdb=" CB ASN B 550 " ideal model delta sigma weight residual 1.524 1.540 -0.016 1.46e-02 4.69e+03 1.15e+00 bond pdb=" N ILE B 533 " pdb=" CA ILE B 533 " ideal model delta sigma weight residual 1.459 1.472 -0.013 1.25e-02 6.40e+03 1.01e+00 bond pdb=" C4 ADP B 601 " pdb=" C5 ADP B 601 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 1.01e+00 bond pdb=" CB ASN B 550 " pdb=" CG ASN B 550 " ideal model delta sigma weight residual 1.516 1.535 -0.019 2.50e-02 1.60e+03 5.92e-01 bond pdb=" CG1 ILE A 36 " pdb=" CD1 ILE A 36 " ideal model delta sigma weight residual 1.513 1.483 0.030 3.90e-02 6.57e+02 5.91e-01 ... (remaining 9257 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 12355 1.51 - 3.02: 151 3.02 - 4.53: 34 4.53 - 6.05: 15 6.05 - 7.56: 3 Bond angle restraints: 12558 Sorted by residual: angle pdb=" CA GLN B 200 " pdb=" CB GLN B 200 " pdb=" CG GLN B 200 " ideal model delta sigma weight residual 114.10 120.06 -5.96 2.00e+00 2.50e-01 8.88e+00 angle pdb=" C ASP B 334 " pdb=" N GLU B 335 " pdb=" CA GLU B 335 " ideal model delta sigma weight residual 121.54 126.37 -4.83 1.91e+00 2.74e-01 6.40e+00 angle pdb=" N ARG A 509 " pdb=" CA ARG A 509 " pdb=" CB ARG A 509 " ideal model delta sigma weight residual 110.16 113.75 -3.59 1.48e+00 4.57e-01 5.90e+00 angle pdb=" N ILE B 509 " pdb=" CA ILE B 509 " pdb=" C ILE B 509 " ideal model delta sigma weight residual 108.82 105.90 2.92 1.22e+00 6.72e-01 5.73e+00 angle pdb=" CG1 ILE B 509 " pdb=" CB ILE B 509 " pdb=" CG2 ILE B 509 " ideal model delta sigma weight residual 110.70 103.58 7.12 3.00e+00 1.11e-01 5.64e+00 ... (remaining 12553 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.47: 5460 32.47 - 64.94: 133 64.94 - 97.41: 9 97.41 - 129.88: 1 129.88 - 162.34: 1 Dihedral angle restraints: 5604 sinusoidal: 2273 harmonic: 3331 Sorted by residual: dihedral pdb=" O2A ADP B 601 " pdb=" O3A ADP B 601 " pdb=" PA ADP B 601 " pdb=" PB ADP B 601 " ideal model delta sinusoidal sigma weight residual -60.00 102.35 -162.34 1 2.00e+01 2.50e-03 4.69e+01 dihedral pdb=" O1B ADP B 601 " pdb=" O3A ADP B 601 " pdb=" PB ADP B 601 " pdb=" PA ADP B 601 " ideal model delta sinusoidal sigma weight residual -60.00 58.86 -118.86 1 2.00e+01 2.50e-03 3.56e+01 dihedral pdb=" CA GLN A 281 " pdb=" C GLN A 281 " pdb=" N ILE A 282 " pdb=" CA ILE A 282 " ideal model delta harmonic sigma weight residual 180.00 -162.48 -17.52 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 5601 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1094 0.037 - 0.075: 297 0.075 - 0.112: 70 0.112 - 0.150: 18 0.150 - 0.187: 2 Chirality restraints: 1481 Sorted by residual: chirality pdb=" CB ILE B 509 " pdb=" CA ILE B 509 " pdb=" CG1 ILE B 509 " pdb=" CG2 ILE B 509 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.19 2.00e-01 2.50e+01 8.75e-01 chirality pdb=" CA ILE B 509 " pdb=" N ILE B 509 " pdb=" C ILE B 509 " pdb=" CB ILE B 509 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.34e-01 chirality pdb=" CG LEU A 505 " pdb=" CB LEU A 505 " pdb=" CD1 LEU A 505 " pdb=" CD2 LEU A 505 " both_signs ideal model delta sigma weight residual False -2.59 -2.74 0.15 2.00e-01 2.50e+01 5.29e-01 ... (remaining 1478 not shown) Planarity restraints: 1572 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 463 " -0.034 5.00e-02 4.00e+02 5.23e-02 4.37e+00 pdb=" N PRO A 464 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 464 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 464 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 200 " -0.008 2.00e-02 2.50e+03 1.65e-02 2.71e+00 pdb=" CD GLN B 200 " 0.028 2.00e-02 2.50e+03 pdb=" OE1 GLN B 200 " -0.011 2.00e-02 2.50e+03 pdb=" NE2 GLN B 200 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 260 " 0.015 2.00e-02 2.50e+03 1.16e-02 2.67e+00 pdb=" CG TYR B 260 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR B 260 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR B 260 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR B 260 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 260 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR B 260 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 260 " 0.000 2.00e-02 2.50e+03 ... (remaining 1569 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 100 2.65 - 3.21: 8655 3.21 - 3.78: 14669 3.78 - 4.34: 20076 4.34 - 4.90: 33596 Nonbonded interactions: 77096 Sorted by model distance: nonbonded pdb=" OG SER A 374 " pdb="MG MG A 702 " model vdw 2.090 2.170 nonbonded pdb=" OE1 GLN A 415 " pdb="MG MG A 702 " model vdw 2.095 2.170 nonbonded pdb=" O3G ATP A 701 " pdb="MG MG A 702 " model vdw 2.097 2.170 nonbonded pdb=" OG SER B 94 " pdb=" OD1 ASN B 133 " model vdw 2.148 3.040 nonbonded pdb=" O TYR A 504 " pdb=" OG SER A 508 " model vdw 2.209 3.040 ... (remaining 77091 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: 1.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.440 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6741 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 : 0.002 0.030 9262 Z= 0.107 Angle : 0.486 7.557 12558 Z= 0.251 Chirality : 0.038 0.187 1481 Planarity : 0.003 0.052 1572 Dihedral : 14.411 162.344 3450 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.76 % Favored : 98.07 % 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: 2.12 (0.25), residues: 1138 helix: 2.21 (0.18), residues: 788 sheet: -0.48 (0.63), residues: 73 loop : -0.42 (0.37), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 509 TYR 0.028 0.001 TYR B 260 PHE 0.014 0.001 PHE B 460 TRP 0.010 0.001 TRP B 196 HIS 0.004 0.001 HIS A 567 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.11 ( 9262) covalent geometry : angle 0.48647 / 0.25 (12558) hydrogen bonds : bond 0.11829 / 8.13 ( 629) hydrogen bonds : angle 4.93426 / 3.72 ( 1854) *********************** 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 179 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.374 Fit side-chains REVERT: A 102 GLU cc_start: 0.6918 (tt0) cc_final: 0.5765 (mp0) REVERT: A 168 LEU cc_start: 0.6887 (mp) cc_final: 0.6554 (mm) REVERT: A 197 GLN cc_start: 0.6683 (tt0) cc_final: 0.5829 (mm-40) REVERT: A 212 GLU cc_start: 0.6815 (mm-30) cc_final: 0.5184 (mp0) REVERT: A 220 THR cc_start: 0.7337 (m) cc_final: 0.6974 (p) REVERT: A 223 LYS cc_start: 0.6873 (mttm) cc_final: 0.6490 (mttt) REVERT: A 256 TRP cc_start: 0.7019 (t60) cc_final: 0.6768 (t60) REVERT: A 266 LEU cc_start: 0.8622 (mp) cc_final: 0.8352 (mt) REVERT: A 314 ASP cc_start: 0.7255 (p0) cc_final: 0.6973 (p0) REVERT: A 325 LYS cc_start: 0.7537 (mptt) cc_final: 0.6918 (mmmm) REVERT: A 337 LYS cc_start: 0.7429 (mmtm) cc_final: 0.6993 (mmpt) REVERT: A 358 PHE cc_start: 0.8108 (m-80) cc_final: 0.7762 (m-80) REVERT: A 362 SER cc_start: 0.8028 (m) cc_final: 0.7389 (p) REVERT: A 421 ARG cc_start: 0.6963 (ttt-90) cc_final: 0.6352 (ttp80) REVERT: B 58 VAL cc_start: 0.6710 (t) cc_final: 0.6382 (m) REVERT: B 102 MET cc_start: 0.7807 (tpt) cc_final: 0.7321 (tpt) REVERT: B 103 MET cc_start: 0.6654 (mtp) cc_final: 0.6414 (mtm) REVERT: B 159 ARG cc_start: 0.5359 (ttp80) cc_final: 0.4904 (ttp-110) REVERT: B 187 TYR cc_start: 0.6458 (t80) cc_final: 0.6138 (t80) REVERT: B 236 ASN cc_start: 0.6854 (m-40) cc_final: 0.6615 (m-40) REVERT: B 389 MET cc_start: 0.7310 (mmp) cc_final: 0.6859 (mmm) REVERT: B 396 LYS cc_start: 0.6763 (mtpt) cc_final: 0.5529 (ttpt) REVERT: B 412 GLU cc_start: 0.5572 (mp0) cc_final: 0.5049 (mp0) REVERT: B 514 GLU cc_start: 0.5578 (tt0) cc_final: 0.5243 (tt0) REVERT: B 518 GLN cc_start: 0.5887 (mm110) cc_final: 0.5306 (mt0) REVERT: B 536 ARG cc_start: 0.6949 (mtp-110) cc_final: 0.6745 (mtp180) REVERT: B 537 LEU cc_start: 0.7094 (mm) cc_final: 0.6769 (OUTLIER) outliers start: 0 outliers final: 1 residues processed: 179 average time/residue: 0.5600 time to fit residues: 107.2998 Evaluate side-chains 134 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.426 ------------------------------------------------------------------------------- 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: 0.6980 chunk 49 optimal weight: 0.0570 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.0020 chunk 100 optimal weight: 0.2980 overall best weight: 0.3106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 277 ASN A 281 GLN A 401 ASN A 427 ASN B 222 GLN B 226 ASN B 440 ASN B 456 ASN B 574 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.170205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.137923 restraints weight = 9154.909| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.26 r_work: 0.3414 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9262 Z= 0.117 Angle : 0.491 6.063 12558 Z= 0.251 Chirality : 0.039 0.180 1481 Planarity : 0.004 0.055 1572 Dihedral : 8.427 163.076 1278 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.85 % Favored : 97.98 % Rotamer: Outliers : 0.60 % Allowed : 9.26 % Favored : 90.13 % 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: 2.21 (0.18), residues: 796 sheet: -0.55 (0.64), residues: 68 loop : -0.47 (0.37), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 154 TYR 0.006 0.001 TYR A 563 PHE 0.015 0.001 PHE B 460 TRP 0.011 0.001 TRP B 196 HIS 0.007 0.001 HIS A 567 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 ( 9262) covalent geometry : angle 0.49060 / 0.25 (12558) hydrogen bonds : bond 0.04058 / 2.69 ( 629) hydrogen bonds : angle 4.15925 / 3.10 ( 1854) *********************** 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 147 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 141 time to evaluate : 0.355 Fit side-chains REVERT: A 102 GLU cc_start: 0.8050 (tt0) cc_final: 0.7145 (mp0) REVERT: A 168 LEU cc_start: 0.8058 (mp) cc_final: 0.7799 (mt) REVERT: A 197 GLN cc_start: 0.8250 (tt0) cc_final: 0.7658 (mm-40) REVERT: A 212 GLU cc_start: 0.7892 (mm-30) cc_final: 0.6919 (mp0) REVERT: A 220 THR cc_start: 0.8557 (m) cc_final: 0.8343 (p) REVERT: A 223 LYS cc_start: 0.8324 (mttm) cc_final: 0.8089 (mttt) REVERT: A 325 LYS cc_start: 0.8043 (mptt) cc_final: 0.7703 (mmmm) REVERT: A 337 LYS cc_start: 0.8193 (mmtm) cc_final: 0.7952 (mmpt) REVERT: A 421 ARG cc_start: 0.7768 (ttt-90) cc_final: 0.7448 (ttp80) REVERT: B 58 VAL cc_start: 0.7754 (t) cc_final: 0.7491 (m) REVERT: B 102 MET cc_start: 0.8863 (tpt) cc_final: 0.8461 (tpt) REVERT: B 159 ARG cc_start: 0.6693 (ttp80) cc_final: 0.6256 (ttp-110) REVERT: B 179 THR cc_start: 0.8461 (m) cc_final: 0.8164 (m) REVERT: B 412 GLU cc_start: 0.6953 (mp0) cc_final: 0.6676 (mp0) REVERT: B 442 LYS cc_start: 0.7575 (ptpp) cc_final: 0.7251 (mmtt) REVERT: B 514 GLU cc_start: 0.6618 (tt0) cc_final: 0.6366 (tt0) REVERT: B 518 GLN cc_start: 0.7496 (mm110) cc_final: 0.6775 (mt0) outliers start: 6 outliers final: 2 residues processed: 142 average time/residue: 0.5853 time to fit residues: 88.5078 Evaluate side-chains 125 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 123 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain B residue 496 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 2 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 54 optimal weight: 0.4980 chunk 18 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 104 optimal weight: 0.9990 chunk 101 optimal weight: 0.0980 chunk 12 optimal weight: 0.6980 chunk 108 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 440 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.166827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.133668 restraints weight = 9094.250| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.28 r_work: 0.3363 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9262 Z= 0.134 Angle : 0.484 6.045 12558 Z= 0.247 Chirality : 0.039 0.147 1481 Planarity : 0.004 0.043 1572 Dihedral : 8.440 165.533 1278 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.49 % Favored : 98.33 % Rotamer: Outliers : 1.61 % Allowed : 10.07 % 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: 2.03 (0.25), residues: 1138 helix: 2.14 (0.18), residues: 796 sheet: -0.65 (0.62), residues: 68 loop : -0.46 (0.38), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 154 TYR 0.007 0.001 TYR A 75 PHE 0.020 0.001 PHE B 460 TRP 0.010 0.001 TRP B 196 HIS 0.005 0.001 HIS A 567 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 ( 9262) covalent geometry : angle 0.48422 / 0.25 (12558) hydrogen bonds : bond 0.04058 / 2.67 ( 629) hydrogen bonds : angle 4.11760 / 3.06 ( 1854) *********************** 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 155 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 139 time to evaluate : 0.374 Fit side-chains REVERT: A 102 GLU cc_start: 0.8015 (tt0) cc_final: 0.7063 (mp0) REVERT: A 168 LEU cc_start: 0.8170 (mp) cc_final: 0.7938 (mt) REVERT: A 197 GLN cc_start: 0.8248 (tt0) cc_final: 0.7560 (mm-40) REVERT: A 212 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7002 (mp0) REVERT: A 223 LYS cc_start: 0.8318 (mttm) cc_final: 0.8077 (mttt) REVERT: A 240 SER cc_start: 0.8415 (t) cc_final: 0.8176 (m) REVERT: A 325 LYS cc_start: 0.8151 (mptt) cc_final: 0.7727 (mmmm) REVERT: A 337 LYS cc_start: 0.8012 (mmtm) cc_final: 0.7746 (mmpt) REVERT: A 421 ARG cc_start: 0.7707 (ttt-90) cc_final: 0.7400 (ttp80) REVERT: A 435 GLU cc_start: 0.6987 (OUTLIER) cc_final: 0.6237 (tm-30) REVERT: B 102 MET cc_start: 0.8884 (tpt) cc_final: 0.8487 (tpt) REVERT: B 157 MET cc_start: 0.8124 (mtt) cc_final: 0.7674 (mtt) REVERT: B 159 ARG cc_start: 0.6717 (ttp80) cc_final: 0.6273 (ttp-110) REVERT: B 179 THR cc_start: 0.8529 (m) cc_final: 0.8197 (m) REVERT: B 396 LYS cc_start: 0.7485 (ttpp) cc_final: 0.7065 (tppt) REVERT: B 402 ASP cc_start: 0.7285 (m-30) cc_final: 0.7049 (m-30) REVERT: B 412 GLU cc_start: 0.7063 (mp0) cc_final: 0.6770 (mp0) REVERT: B 442 LYS cc_start: 0.7506 (ptpp) cc_final: 0.7239 (mmtt) REVERT: B 525 MET cc_start: 0.7894 (OUTLIER) cc_final: 0.6722 (mtp) outliers start: 16 outliers final: 4 residues processed: 148 average time/residue: 0.5561 time to fit residues: 87.4772 Evaluate side-chains 134 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 128 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 525 MET Chi-restraints excluded: chain B residue 532 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 85 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 112 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 88 optimal weight: 0.2980 chunk 101 optimal weight: 4.9990 chunk 43 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 427 ASN B 440 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.164276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.131471 restraints weight = 9158.036| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 1.24 r_work: 0.3357 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9262 Z= 0.156 Angle : 0.505 6.033 12558 Z= 0.258 Chirality : 0.040 0.170 1481 Planarity : 0.004 0.039 1572 Dihedral : 8.507 168.422 1278 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.42 % Allowed : 11.18 % Favored : 86.40 % 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: 1.79 (0.25), residues: 1138 helix: 1.94 (0.18), residues: 795 sheet: -0.71 (0.62), residues: 67 loop : -0.51 (0.37), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 154 TYR 0.008 0.001 TYR B 86 PHE 0.019 0.001 PHE B 460 TRP 0.011 0.001 TRP B 196 HIS 0.004 0.001 HIS A 567 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 ( 9262) covalent geometry : angle 0.50461 / 0.26 (12558) hydrogen bonds : bond 0.04142 / 2.71 ( 629) hydrogen bonds : angle 4.17511 / 3.10 ( 1854) *********************** 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 159 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 135 time to evaluate : 0.247 Fit side-chains REVERT: A 102 GLU cc_start: 0.8038 (tt0) cc_final: 0.7145 (mp0) REVERT: A 115 ARG cc_start: 0.7743 (OUTLIER) cc_final: 0.7016 (mtp180) REVERT: A 168 LEU cc_start: 0.8286 (mp) cc_final: 0.8081 (mt) REVERT: A 197 GLN cc_start: 0.8280 (tt0) cc_final: 0.7637 (mm-40) REVERT: A 212 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7236 (mp0) REVERT: A 223 LYS cc_start: 0.8333 (mttm) cc_final: 0.8091 (mttt) REVERT: A 421 ARG cc_start: 0.7804 (ttt-90) cc_final: 0.7457 (ttp80) REVERT: A 435 GLU cc_start: 0.7045 (OUTLIER) cc_final: 0.6364 (tm-30) REVERT: A 470 ARG cc_start: 0.7326 (mpt-90) cc_final: 0.6991 (mpp80) REVERT: B 102 MET cc_start: 0.8845 (tpt) cc_final: 0.8440 (tpt) REVERT: B 159 ARG cc_start: 0.6834 (ttp80) cc_final: 0.6338 (ttp-110) REVERT: B 179 THR cc_start: 0.8596 (m) cc_final: 0.8247 (m) REVERT: B 412 GLU cc_start: 0.7269 (mp0) cc_final: 0.6972 (mp0) REVERT: B 442 LYS cc_start: 0.7558 (ptpp) cc_final: 0.7303 (mmtt) REVERT: B 525 MET cc_start: 0.8015 (OUTLIER) cc_final: 0.6975 (mtp) REVERT: B 549 MET cc_start: 0.6053 (OUTLIER) cc_final: 0.5663 (mtp) outliers start: 24 outliers final: 11 residues processed: 152 average time/residue: 0.5605 time to fit residues: 90.6221 Evaluate side-chains 144 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 525 MET Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 549 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 63 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 chunk 1 optimal weight: 0.1980 chunk 60 optimal weight: 0.9990 chunk 85 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 89 optimal weight: 7.9990 chunk 7 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 440 ASN B 463 GLN B 518 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.147198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.109951 restraints weight = 9506.464| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.44 r_work: 0.3047 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9262 Z= 0.144 Angle : 0.492 6.041 12558 Z= 0.252 Chirality : 0.039 0.180 1481 Planarity : 0.004 0.043 1572 Dihedral : 8.509 170.020 1278 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.91 % Allowed : 13.19 % Favored : 84.89 % 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: 1.81 (0.25), residues: 1138 helix: 1.95 (0.18), residues: 797 sheet: -0.62 (0.63), residues: 67 loop : -0.48 (0.37), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 154 TYR 0.007 0.001 TYR A 75 PHE 0.017 0.001 PHE B 460 TRP 0.012 0.001 TRP B 196 HIS 0.004 0.001 HIS B 560 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 ( 9262) covalent geometry : angle 0.49184 / 0.25 (12558) hydrogen bonds : bond 0.04047 / 2.64 ( 629) hydrogen bonds : angle 4.15054 / 3.08 ( 1854) *********************** 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 151 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 0.350 Fit side-chains REVERT: A 102 GLU cc_start: 0.7702 (tt0) cc_final: 0.6381 (mp0) REVERT: A 168 LEU cc_start: 0.7975 (mp) cc_final: 0.7774 (tp) REVERT: A 197 GLN cc_start: 0.7972 (tt0) cc_final: 0.7074 (mm-40) REVERT: A 212 GLU cc_start: 0.7988 (mm-30) cc_final: 0.6604 (mp0) REVERT: A 223 LYS cc_start: 0.7928 (mttm) cc_final: 0.7558 (mttt) REVERT: A 337 LYS cc_start: 0.8183 (mmpt) cc_final: 0.7971 (mmpt) REVERT: A 421 ARG cc_start: 0.7538 (ttt-90) cc_final: 0.6954 (ttp80) REVERT: A 435 GLU cc_start: 0.6808 (OUTLIER) cc_final: 0.6017 (tm-30) REVERT: A 470 ARG cc_start: 0.7259 (mpt-90) cc_final: 0.6846 (mpt-90) REVERT: B 102 MET cc_start: 0.8667 (tpt) cc_final: 0.8310 (tpt) REVERT: B 159 ARG cc_start: 0.6460 (ttp80) cc_final: 0.6040 (ttp-110) REVERT: B 179 THR cc_start: 0.8243 (m) cc_final: 0.7901 (m) REVERT: B 202 GLN cc_start: 0.7456 (mt0) cc_final: 0.7182 (mt0) REVERT: B 412 GLU cc_start: 0.6763 (mp0) cc_final: 0.6258 (mp0) REVERT: B 442 LYS cc_start: 0.7341 (ptpp) cc_final: 0.6913 (mmtt) REVERT: B 525 MET cc_start: 0.7693 (OUTLIER) cc_final: 0.6844 (mtp) outliers start: 19 outliers final: 11 residues processed: 146 average time/residue: 0.5126 time to fit residues: 79.5620 Evaluate side-chains 138 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 125 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain B residue 525 MET Chi-restraints excluded: chain B residue 532 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 21 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 37 optimal weight: 0.0060 chunk 11 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 41 optimal weight: 0.0070 chunk 13 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 96 optimal weight: 0.0370 chunk 22 optimal weight: 0.6980 overall best weight: 0.2892 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 440 ASN B 463 GLN B 518 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.150124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.113292 restraints weight = 9492.523| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.44 r_work: 0.3102 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9262 Z= 0.107 Angle : 0.458 6.042 12558 Z= 0.235 Chirality : 0.038 0.183 1481 Planarity : 0.004 0.047 1572 Dihedral : 8.351 169.606 1278 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.51 % Allowed : 14.20 % Favored : 84.29 % 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: 2.02 (0.25), residues: 1138 helix: 2.11 (0.18), residues: 797 sheet: -0.52 (0.63), residues: 67 loop : -0.45 (0.38), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 154 TYR 0.011 0.001 TYR B 409 PHE 0.016 0.001 PHE B 460 TRP 0.012 0.001 TRP B 196 HIS 0.003 0.001 HIS B 560 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 ( 9262) covalent geometry : angle 0.45812 / 0.24 (12558) hydrogen bonds : bond 0.03745 / 2.43 ( 629) hydrogen bonds : angle 4.00914 / 2.97 ( 1854) *********************** 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 147 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 0.366 Fit side-chains REVERT: A 102 GLU cc_start: 0.7667 (tt0) cc_final: 0.6388 (mp0) REVERT: A 197 GLN cc_start: 0.7984 (tt0) cc_final: 0.7072 (mm-40) REVERT: A 212 GLU cc_start: 0.7954 (mm-30) cc_final: 0.6581 (mp0) REVERT: A 223 LYS cc_start: 0.7950 (mttm) cc_final: 0.7634 (mttt) REVERT: A 421 ARG cc_start: 0.7587 (ttt-90) cc_final: 0.7039 (ttp80) REVERT: A 435 GLU cc_start: 0.6792 (OUTLIER) cc_final: 0.6013 (tm-30) REVERT: A 470 ARG cc_start: 0.7285 (mpt-90) cc_final: 0.6859 (mpt-90) REVERT: B 157 MET cc_start: 0.7747 (mtt) cc_final: 0.7283 (mtt) REVERT: B 159 ARG cc_start: 0.6410 (ttp80) cc_final: 0.6019 (ttp-110) REVERT: B 179 THR cc_start: 0.8253 (m) cc_final: 0.7928 (m) REVERT: B 236 ASN cc_start: 0.7949 (m-40) cc_final: 0.7612 (m-40) REVERT: B 412 GLU cc_start: 0.6600 (mp0) cc_final: 0.6173 (mp0) REVERT: B 442 LYS cc_start: 0.7179 (ptpp) cc_final: 0.6710 (mmtt) outliers start: 15 outliers final: 7 residues processed: 143 average time/residue: 0.5766 time to fit residues: 87.7640 Evaluate side-chains 134 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 126 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain B residue 532 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 53 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 50 optimal weight: 5.9990 chunk 59 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 0.2980 chunk 66 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 440 ASN B 463 GLN B 518 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.145698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.109990 restraints weight = 9564.551| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.35 r_work: 0.3035 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9262 Z= 0.175 Angle : 0.523 6.090 12558 Z= 0.266 Chirality : 0.040 0.200 1481 Planarity : 0.004 0.044 1572 Dihedral : 8.588 175.723 1278 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.91 % Allowed : 14.70 % 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: 1.76 (0.25), residues: 1138 helix: 1.90 (0.18), residues: 797 sheet: -0.59 (0.63), residues: 67 loop : -0.49 (0.37), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 154 TYR 0.009 0.001 TYR A 75 PHE 0.018 0.002 PHE B 460 TRP 0.012 0.001 TRP B 196 HIS 0.005 0.001 HIS B 560 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.17 ( 9262) covalent geometry : angle 0.52338 / 0.27 (12558) hydrogen bonds : bond 0.04203 / 2.74 ( 629) hydrogen bonds : angle 4.18766 / 3.10 ( 1854) *********************** 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 154 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 135 time to evaluate : 0.359 Fit side-chains REVERT: A 42 ILE cc_start: 0.8416 (OUTLIER) cc_final: 0.8203 (mt) REVERT: A 102 GLU cc_start: 0.7711 (tt0) cc_final: 0.6440 (mp0) REVERT: A 115 ARG cc_start: 0.7606 (OUTLIER) cc_final: 0.6786 (mtp180) REVERT: A 197 GLN cc_start: 0.7984 (tt0) cc_final: 0.7064 (mm-40) REVERT: A 212 GLU cc_start: 0.8017 (mm-30) cc_final: 0.6639 (mp0) REVERT: A 223 LYS cc_start: 0.7929 (mttm) cc_final: 0.7557 (mttt) REVERT: A 421 ARG cc_start: 0.7591 (ttt-90) cc_final: 0.6991 (ttp80) REVERT: A 435 GLU cc_start: 0.6841 (OUTLIER) cc_final: 0.6040 (tm-30) REVERT: A 470 ARG cc_start: 0.7287 (mpt-90) cc_final: 0.6985 (mpt-90) REVERT: B 159 ARG cc_start: 0.6430 (ttp80) cc_final: 0.5974 (ttp-110) REVERT: B 179 THR cc_start: 0.8338 (m) cc_final: 0.7989 (m) REVERT: B 412 GLU cc_start: 0.6775 (mp0) cc_final: 0.6282 (mp0) REVERT: B 424 GLU cc_start: 0.7566 (mm-30) cc_final: 0.6356 (mp0) REVERT: B 442 LYS cc_start: 0.7357 (ptpp) cc_final: 0.6956 (mmtt) REVERT: B 525 MET cc_start: 0.7378 (mtp) cc_final: 0.6912 (mtp) outliers start: 19 outliers final: 10 residues processed: 149 average time/residue: 0.5322 time to fit residues: 84.4814 Evaluate side-chains 140 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 127 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain B residue 102 MET Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain B residue 532 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 87 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 297 ASN B 440 ASN B 463 GLN B 518 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.146334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.108539 restraints weight = 9480.790| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 1.49 r_work: 0.3027 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9262 Z= 0.155 Angle : 0.510 6.074 12558 Z= 0.260 Chirality : 0.040 0.204 1481 Planarity : 0.004 0.051 1572 Dihedral : 8.608 176.570 1278 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.32 % Allowed : 14.10 % Favored : 83.59 % 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: 1.74 (0.25), residues: 1138 helix: 1.88 (0.18), residues: 797 sheet: -0.55 (0.64), residues: 67 loop : -0.49 (0.37), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 154 TYR 0.007 0.001 TYR B 86 PHE 0.018 0.001 PHE B 460 TRP 0.013 0.001 TRP B 196 HIS 0.004 0.001 HIS B 560 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.15 ( 9262) covalent geometry : angle 0.50973 / 0.26 (12558) hydrogen bonds : bond 0.04090 / 2.67 ( 629) hydrogen bonds : angle 4.16921 / 3.09 ( 1854) *********************** 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 148 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 0.250 Fit side-chains REVERT: A 102 GLU cc_start: 0.7743 (tt0) cc_final: 0.6401 (mp0) REVERT: A 115 ARG cc_start: 0.7613 (OUTLIER) cc_final: 0.7160 (mtt180) REVERT: A 197 GLN cc_start: 0.8027 (tt0) cc_final: 0.7088 (mm-40) REVERT: A 212 GLU cc_start: 0.8061 (mm-30) cc_final: 0.6603 (mp0) REVERT: A 223 LYS cc_start: 0.7921 (mttm) cc_final: 0.7550 (mttt) REVERT: A 421 ARG cc_start: 0.7631 (ttt-90) cc_final: 0.7022 (ttp80) REVERT: A 470 ARG cc_start: 0.7273 (mpt-90) cc_final: 0.6937 (mpt-90) REVERT: B 159 ARG cc_start: 0.6428 (ttp80) cc_final: 0.5971 (ttp-110) REVERT: B 179 THR cc_start: 0.8291 (m) cc_final: 0.7947 (m) REVERT: B 202 GLN cc_start: 0.7502 (mt0) cc_final: 0.7250 (mt0) REVERT: B 412 GLU cc_start: 0.6761 (mp0) cc_final: 0.6310 (mp0) REVERT: B 424 GLU cc_start: 0.7572 (mm-30) cc_final: 0.6351 (mp0) REVERT: B 442 LYS cc_start: 0.7170 (ptpp) cc_final: 0.6702 (mmtt) REVERT: B 525 MET cc_start: 0.7463 (mtp) cc_final: 0.7020 (mtp) outliers start: 23 outliers final: 13 residues processed: 142 average time/residue: 0.5634 time to fit residues: 84.8758 Evaluate side-chains 135 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 459 PHE Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 559 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 97 optimal weight: 0.7980 chunk 79 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 36 optimal weight: 0.4980 chunk 69 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 440 ASN B 463 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.146267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.108536 restraints weight = 9499.886| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.48 r_work: 0.3033 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9262 Z= 0.155 Angle : 0.520 6.751 12558 Z= 0.266 Chirality : 0.040 0.205 1481 Planarity : 0.004 0.051 1572 Dihedral : 8.649 178.045 1278 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.71 % Allowed : 14.90 % 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: 1.71 (0.25), residues: 1138 helix: 1.85 (0.18), residues: 797 sheet: -0.57 (0.63), residues: 67 loop : -0.47 (0.37), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 154 TYR 0.009 0.001 TYR B 86 PHE 0.018 0.001 PHE B 460 TRP 0.013 0.001 TRP B 196 HIS 0.004 0.001 HIS B 560 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 ( 9262) covalent geometry : angle 0.52025 / 0.27 (12558) hydrogen bonds : bond 0.04086 / 2.66 ( 629) hydrogen bonds : angle 4.19124 / 3.10 ( 1854) *********************** 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 141 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 0.380 Fit side-chains REVERT: A 40 VAL cc_start: 0.7984 (OUTLIER) cc_final: 0.7771 (m) REVERT: A 102 GLU cc_start: 0.7747 (tt0) cc_final: 0.6398 (mp0) REVERT: A 115 ARG cc_start: 0.7610 (OUTLIER) cc_final: 0.7155 (mtt180) REVERT: A 197 GLN cc_start: 0.8029 (tt0) cc_final: 0.7081 (mm-40) REVERT: A 212 GLU cc_start: 0.8130 (mm-30) cc_final: 0.6670 (mp0) REVERT: A 223 LYS cc_start: 0.7920 (mttm) cc_final: 0.7552 (mttt) REVERT: A 421 ARG cc_start: 0.7640 (ttt-90) cc_final: 0.7032 (ttp80) REVERT: A 470 ARG cc_start: 0.7293 (mpt-90) cc_final: 0.6932 (mpt-90) REVERT: B 159 ARG cc_start: 0.6414 (ttp80) cc_final: 0.5952 (ttp-110) REVERT: B 179 THR cc_start: 0.8346 (m) cc_final: 0.8000 (m) REVERT: B 412 GLU cc_start: 0.6756 (mp0) cc_final: 0.6298 (mp0) REVERT: B 424 GLU cc_start: 0.7595 (mm-30) cc_final: 0.6353 (mp0) REVERT: B 442 LYS cc_start: 0.7158 (ptpp) cc_final: 0.6696 (mmtt) REVERT: B 525 MET cc_start: 0.7471 (mtp) cc_final: 0.7034 (mtp) outliers start: 17 outliers final: 15 residues processed: 138 average time/residue: 0.6264 time to fit residues: 91.5867 Evaluate side-chains 136 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 459 PHE Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 559 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 65 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 98 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 101 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 440 ASN B 463 GLN B 518 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.145372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.107583 restraints weight = 9434.654| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 1.48 r_work: 0.3012 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9262 Z= 0.170 Angle : 0.535 7.052 12558 Z= 0.273 Chirality : 0.041 0.218 1481 Planarity : 0.004 0.052 1572 Dihedral : 8.744 179.438 1278 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.91 % Allowed : 14.60 % Favored : 83.48 % 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: 1.61 (0.25), residues: 1138 helix: 1.77 (0.18), residues: 795 sheet: -0.63 (0.63), residues: 67 loop : -0.47 (0.37), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 154 TYR 0.009 0.001 TYR B 86 PHE 0.019 0.002 PHE B 460 TRP 0.013 0.001 TRP B 196 HIS 0.005 0.001 HIS B 560 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.17 ( 9262) covalent geometry : angle 0.53476 / 0.27 (12558) hydrogen bonds : bond 0.04201 / 2.74 ( 629) hydrogen bonds : angle 4.24137 / 3.14 ( 1854) ********************** 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 141 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 0.360 Fit side-chains REVERT: A 40 VAL cc_start: 0.8065 (OUTLIER) cc_final: 0.7831 (m) REVERT: A 42 ILE cc_start: 0.8345 (OUTLIER) cc_final: 0.8121 (mt) REVERT: A 102 GLU cc_start: 0.7720 (tt0) cc_final: 0.6419 (mp0) REVERT: A 115 ARG cc_start: 0.7670 (OUTLIER) cc_final: 0.6965 (mtp180) REVERT: A 197 GLN cc_start: 0.8027 (tt0) cc_final: 0.7075 (mm-40) REVERT: A 212 GLU cc_start: 0.8165 (mm-30) cc_final: 0.6707 (mp0) REVERT: A 223 LYS cc_start: 0.7920 (mttm) cc_final: 0.7548 (mttt) REVERT: A 271 MET cc_start: 0.8597 (mmt) cc_final: 0.8359 (mmp) REVERT: A 421 ARG cc_start: 0.7642 (ttt-90) cc_final: 0.7019 (ttp80) REVERT: A 470 ARG cc_start: 0.7261 (mpt-90) cc_final: 0.6871 (mpt-90) REVERT: B 63 ARG cc_start: 0.7382 (mtm110) cc_final: 0.6980 (ttm170) REVERT: B 159 ARG cc_start: 0.6390 (ttp80) cc_final: 0.5933 (ttp-110) REVERT: B 412 GLU cc_start: 0.6781 (mp0) cc_final: 0.6307 (mp0) REVERT: B 424 GLU cc_start: 0.7592 (mm-30) cc_final: 0.6343 (mp0) REVERT: B 442 LYS cc_start: 0.7147 (ptpp) cc_final: 0.6721 (mmtt) REVERT: B 525 MET cc_start: 0.7524 (mtp) cc_final: 0.7077 (mtp) outliers start: 19 outliers final: 16 residues processed: 135 average time/residue: 0.6247 time to fit residues: 89.4629 Evaluate side-chains 137 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 459 PHE Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 559 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 16 optimal weight: 0.0670 chunk 87 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 84 optimal weight: 0.5980 chunk 83 optimal weight: 0.3980 chunk 42 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 107 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 440 ASN B 463 GLN B 518 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.147447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.110476 restraints weight = 9433.041| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 1.42 r_work: 0.3054 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9262 Z= 0.131 Angle : 0.499 7.182 12558 Z= 0.256 Chirality : 0.039 0.207 1481 Planarity : 0.004 0.059 1572 Dihedral : 8.638 179.876 1278 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.61 % Allowed : 15.11 % 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: 1.80 (0.25), residues: 1138 helix: 1.90 (0.18), residues: 797 sheet: -0.53 (0.64), residues: 67 loop : -0.39 (0.38), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 154 TYR 0.008 0.001 TYR B 86 PHE 0.018 0.001 PHE B 460 TRP 0.014 0.001 TRP B 196 HIS 0.004 0.001 HIS B 560 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 9262) covalent geometry : angle 0.49918 / 0.26 (12558) hydrogen bonds : bond 0.03944 / 2.56 ( 629) hydrogen bonds : angle 4.13566 / 3.06 ( 1854) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3001.69 seconds wall clock time: 51 minutes 52.56 seconds (3112.56 seconds total)