Starting phenix.real_space_refine on Sun May 11 10:31:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u62_41941/05_2025/8u62_41941.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u62_41941/05_2025/8u62_41941.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u62_41941/05_2025/8u62_41941.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u62_41941/05_2025/8u62_41941.map" model { file = "/net/cci-nas-00/data/ceres_data/8u62_41941/05_2025/8u62_41941.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u62_41941/05_2025/8u62_41941.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.019 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 46 5.16 5 C 4977 2.51 5 N 1374 2.21 5 O 1487 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 7884 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 3958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3958 Classifications: {'peptide': 507} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 480} Chain breaks: 2 Chain: "A" Number of atoms: 3840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3840 Classifications: {'peptide': 491} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 464} Chain breaks: 3 Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'LBV': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'LBV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.52, per 1000 atoms: 0.83 Number of scatterers: 7884 At special positions: 0 Unit cell: (85.41, 117.603, 130.743, 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 46 16.00 O 1487 8.00 N 1374 7.00 C 4977 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.07 Conformation dependent library (CDL) restraints added in 858.1 milliseconds 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1876 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 7 sheets defined 48.2% alpha, 16.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'B' and resid 2 through 15 removed outlier: 3.702A pdb=" N ALA B 8 " --> pdb=" O LEU B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 51 No H-bonds generated for 'chain 'B' and resid 49 through 51' Processing helix chain 'B' and resid 57 through 62 removed outlier: 3.832A pdb=" N LEU B 61 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ALA B 62 " --> pdb=" O PRO B 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 57 through 62' Processing helix chain 'B' and resid 66 through 71 Processing helix chain 'B' and resid 71 through 83 Processing helix chain 'B' and resid 130 through 145 Processing helix chain 'B' and resid 148 through 165 Processing helix chain 'B' and resid 200 through 204 Processing helix chain 'B' and resid 205 through 215 Processing helix chain 'B' and resid 253 through 264 Processing helix chain 'B' and resid 294 through 342 removed outlier: 3.528A pdb=" N GLN B 306 " --> pdb=" O GLN B 302 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ASP B 342 " --> pdb=" O MET B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 352 removed outlier: 3.883A pdb=" N GLN B 352 " --> pdb=" O GLY B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 361 removed outlier: 3.628A pdb=" N ASP B 358 " --> pdb=" O GLN B 354 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL B 360 " --> pdb=" O LEU B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 396 removed outlier: 3.605A pdb=" N THR B 390 " --> pdb=" O ARG B 386 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TRP B 391 " --> pdb=" O ALA B 387 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N MET B 392 " --> pdb=" O LEU B 388 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLY B 395 " --> pdb=" O TRP B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 446 removed outlier: 4.147A pdb=" N SER B 445 " --> pdb=" O GLU B 441 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL B 446 " --> pdb=" O VAL B 442 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 441 through 446' Processing helix chain 'B' and resid 468 through 480 Processing helix chain 'B' and resid 488 through 513 Processing helix chain 'B' and resid 513 through 526 removed outlier: 3.909A pdb=" N ALA B 517 " --> pdb=" O LYS B 513 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG B 521 " --> pdb=" O ALA B 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 4 through 15 removed outlier: 3.502A pdb=" N ALA A 14 " --> pdb=" O GLU A 10 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASN A 15 " --> pdb=" O VAL A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 52 removed outlier: 3.549A pdb=" N GLN A 51 " --> pdb=" O ALA A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 62 removed outlier: 3.511A pdb=" N ALA A 62 " --> pdb=" O PRO A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 69 Processing helix chain 'A' and resid 71 through 82 Processing helix chain 'A' and resid 130 through 146 Processing helix chain 'A' and resid 148 through 165 Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'A' and resid 205 through 214 Processing helix chain 'A' and resid 253 through 264 Processing helix chain 'A' and resid 294 through 340 removed outlier: 3.601A pdb=" N THR A 340 " --> pdb=" O GLN A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 352 Processing helix chain 'A' and resid 353 through 361 removed outlier: 3.545A pdb=" N MET A 357 " --> pdb=" O PRO A 353 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL A 360 " --> pdb=" O LEU A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 396 removed outlier: 3.579A pdb=" N ALA A 387 " --> pdb=" O SER A 383 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TRP A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N MET A 392 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET A 393 " --> pdb=" O HIS A 389 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA A 394 " --> pdb=" O THR A 390 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY A 395 " --> pdb=" O TRP A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 409 removed outlier: 3.972A pdb=" N VAL A 408 " --> pdb=" O HIS A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 446 removed outlier: 3.533A pdb=" N VAL A 446 " --> pdb=" O LYS A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 480 Processing helix chain 'A' and resid 488 through 517 removed outlier: 3.562A pdb=" N ALA A 495 " --> pdb=" O ASP A 491 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA A 517 " --> pdb=" O LYS A 513 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 26 through 27 removed outlier: 6.575A pdb=" N THR B 35 " --> pdb=" O LEU B 44 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N VAL B 46 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU B 33 " --> pdb=" O VAL B 46 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LEU B 93 " --> pdb=" O ALA B 104 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 198 through 199 removed outlier: 6.629A pdb=" N ILE B 171 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLU B 185 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL B 169 " --> pdb=" O GLU B 185 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N TRP B 280 " --> pdb=" O PHE B 174 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N LEU B 273 " --> pdb=" O TRP B 280 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N LEU B 282 " --> pdb=" O VAL B 271 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL B 271 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N SER B 284 " --> pdb=" O MET B 269 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N MET B 269 " --> pdb=" O SER B 284 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLY B 286 " --> pdb=" O SER B 267 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N SER B 267 " --> pdb=" O GLY B 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 372 through 377 removed outlier: 3.800A pdb=" N GLY B 364 " --> pdb=" O PHE B 438 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE B 436 " --> pdb=" O ALA B 366 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 26 through 27 Processing sheet with id=AA5, first strand: chain 'A' and resid 43 through 46 removed outlier: 6.366A pdb=" N THR A 35 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL A 46 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LEU A 33 " --> pdb=" O VAL A 46 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 198 through 199 removed outlier: 6.693A pdb=" N ILE A 171 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLU A 185 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N VAL A 169 " --> pdb=" O GLU A 185 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N TRP A 280 " --> pdb=" O PHE A 174 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N LEU A 273 " --> pdb=" O TRP A 280 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N LEU A 282 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL A 271 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N SER A 284 " --> pdb=" O MET A 269 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N MET A 269 " --> pdb=" O SER A 284 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLY A 286 " --> pdb=" O SER A 267 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N SER A 267 " --> pdb=" O GLY A 286 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 373 through 377 removed outlier: 3.717A pdb=" N GLY A 364 " --> pdb=" O PHE A 438 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY A 421 " --> pdb=" O ARG A 439 " (cutoff:3.500A) 424 hydrogen bonds defined for protein. 1182 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.28 Time building geometry restraints manager: 2.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1472 1.32 - 1.45: 1938 1.45 - 1.57: 4555 1.57 - 1.69: 0 1.69 - 1.82: 78 Bond restraints: 8043 Sorted by residual: bond pdb=" C GLU A 38 " pdb=" N PRO A 39 " ideal model delta sigma weight residual 1.334 1.364 -0.030 2.34e-02 1.83e+03 1.65e+00 bond pdb=" CA GLN A 240 " pdb=" CB GLN A 240 " ideal model delta sigma weight residual 1.534 1.552 -0.019 1.78e-02 3.16e+03 1.11e+00 bond pdb=" CB TRP A 391 " pdb=" CG TRP A 391 " ideal model delta sigma weight residual 1.498 1.530 -0.032 3.10e-02 1.04e+03 1.06e+00 bond pdb=" CB GLU A 40 " pdb=" CG GLU A 40 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.32e-01 bond pdb=" CA GLU A 369 " pdb=" CB GLU A 369 " ideal model delta sigma weight residual 1.534 1.558 -0.023 2.47e-02 1.64e+03 8.87e-01 ... (remaining 8038 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 10808 2.53 - 5.07: 99 5.07 - 7.60: 12 7.60 - 10.13: 8 10.13 - 12.66: 1 Bond angle restraints: 10928 Sorted by residual: angle pdb=" CA MET A 139 " pdb=" CB MET A 139 " pdb=" CG MET A 139 " ideal model delta sigma weight residual 114.10 121.72 -7.62 2.00e+00 2.50e-01 1.45e+01 angle pdb=" N GLU A 413 " pdb=" CA GLU A 413 " pdb=" C GLU A 413 " ideal model delta sigma weight residual 114.56 109.82 4.74 1.27e+00 6.20e-01 1.39e+01 angle pdb=" CA LEU A 113 " pdb=" CB LEU A 113 " pdb=" CG LEU A 113 " ideal model delta sigma weight residual 116.30 128.96 -12.66 3.50e+00 8.16e-02 1.31e+01 angle pdb=" CB MET A 139 " pdb=" CG MET A 139 " pdb=" SD MET A 139 " ideal model delta sigma weight residual 112.70 122.56 -9.86 3.00e+00 1.11e-01 1.08e+01 angle pdb=" CA GLU A 369 " pdb=" CB GLU A 369 " pdb=" CG GLU A 369 " ideal model delta sigma weight residual 114.10 120.46 -6.36 2.00e+00 2.50e-01 1.01e+01 ... (remaining 10923 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 4145 17.98 - 35.96: 525 35.96 - 53.93: 155 53.93 - 71.91: 43 71.91 - 89.89: 14 Dihedral angle restraints: 4882 sinusoidal: 1991 harmonic: 2891 Sorted by residual: dihedral pdb=" CA ILE B 368 " pdb=" C ILE B 368 " pdb=" N GLU B 369 " pdb=" CA GLU B 369 " ideal model delta harmonic sigma weight residual 180.00 163.27 16.73 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CG ARG A 322 " pdb=" CD ARG A 322 " pdb=" NE ARG A 322 " pdb=" CZ ARG A 322 " ideal model delta sinusoidal sigma weight residual 90.00 45.03 44.97 2 1.50e+01 4.44e-03 1.07e+01 dihedral pdb=" CG ARG B 162 " pdb=" CD ARG B 162 " pdb=" NE ARG B 162 " pdb=" CZ ARG B 162 " ideal model delta sinusoidal sigma weight residual 180.00 136.01 43.99 2 1.50e+01 4.44e-03 1.03e+01 ... (remaining 4879 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 796 0.033 - 0.065: 295 0.065 - 0.098: 82 0.098 - 0.130: 43 0.130 - 0.163: 9 Chirality restraints: 1225 Sorted by residual: chirality pdb=" CG LEU A 113 " pdb=" CB LEU A 113 " pdb=" CD1 LEU A 113 " pdb=" CD2 LEU A 113 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.61e-01 chirality pdb=" CG LEU A 117 " pdb=" CB LEU A 117 " pdb=" CD1 LEU A 117 " pdb=" CD2 LEU A 117 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.37e-01 chirality pdb=" CA ILE A 220 " pdb=" N ILE A 220 " pdb=" C ILE A 220 " pdb=" CB ILE A 220 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.23e-01 ... (remaining 1222 not shown) Planarity restraints: 1423 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 391 " -0.016 2.00e-02 2.50e+03 1.36e-02 4.64e+00 pdb=" CG TRP A 391 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP A 391 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP A 391 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 391 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 391 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 391 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 391 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 391 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 391 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 40 " -0.008 2.00e-02 2.50e+03 1.65e-02 2.71e+00 pdb=" C GLU A 40 " 0.028 2.00e-02 2.50e+03 pdb=" O GLU A 40 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU A 41 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 410 " 0.027 5.00e-02 4.00e+02 4.08e-02 2.66e+00 pdb=" N PRO A 411 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 411 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 411 " 0.023 5.00e-02 4.00e+02 ... (remaining 1420 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 307 2.72 - 3.26: 7758 3.26 - 3.81: 12860 3.81 - 4.35: 14986 4.35 - 4.90: 25833 Nonbonded interactions: 61744 Sorted by model distance: nonbonded pdb=" OH TYR B 225 " pdb=" OG SER B 251 " model vdw 2.175 3.040 nonbonded pdb=" O GLN A 416 " pdb=" OG SER A 420 " model vdw 2.188 3.040 nonbonded pdb=" O ALA A 387 " pdb=" OG1 THR A 390 " model vdw 2.235 3.040 nonbonded pdb=" OG SER A 47 " pdb=" OD1 ASN A 49 " model vdw 2.246 3.040 nonbonded pdb=" OE1 GLU A 381 " pdb=" OG SER A 383 " model vdw 2.274 3.040 ... (remaining 61739 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 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 3 through 123 or resid 129 through 340 or resid 345 throug \ h 517 or resid 900)) } 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: 6.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.110 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 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 0.067 8045 Z= 0.177 Angle : 0.614 12.663 10928 Z= 0.296 Chirality : 0.042 0.163 1225 Planarity : 0.004 0.041 1423 Dihedral : 18.211 89.888 3006 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.59 % Allowed : 31.02 % Favored : 68.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.28), residues: 984 helix: 1.50 (0.26), residues: 414 sheet: -0.07 (0.39), residues: 169 loop : 0.19 (0.35), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP A 391 HIS 0.015 0.001 HIS A 295 PHE 0.010 0.001 PHE B 34 TYR 0.025 0.001 TYR A 409 ARG 0.009 0.000 ARG A 322 Details of bonding type rmsd hydrogen bonds : bond 0.22741 ( 424) hydrogen bonds : angle 6.90400 ( 1182) covalent geometry : bond 0.00323 ( 8043) covalent geometry : angle 0.61393 (10928) Misc. bond : bond 0.06558 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 190 time to evaluate : 0.795 Fit side-chains revert: symmetry clash REVERT: B 79 ARG cc_start: 0.8378 (ttm110) cc_final: 0.8020 (ptp-110) REVERT: B 337 MET cc_start: 0.7501 (tpp) cc_final: 0.7193 (tpp) REVERT: B 370 ASP cc_start: 0.6754 (m-30) cc_final: 0.6549 (m-30) outliers start: 5 outliers final: 3 residues processed: 192 average time/residue: 0.2299 time to fit residues: 57.2516 Evaluate side-chains 193 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 190 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 275 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 chunk 41 optimal weight: 0.4980 chunk 25 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 89 optimal weight: 0.0040 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 120 GLN A 275 GLN A 505 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.149937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.128955 restraints weight = 11850.662| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.74 r_work: 0.3490 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8045 Z= 0.162 Angle : 0.560 7.878 10928 Z= 0.281 Chirality : 0.042 0.153 1225 Planarity : 0.004 0.041 1423 Dihedral : 5.772 55.169 1124 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 4.70 % Allowed : 26.44 % Favored : 68.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.28), residues: 984 helix: 2.12 (0.25), residues: 429 sheet: 0.17 (0.40), residues: 167 loop : 0.11 (0.36), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 391 HIS 0.009 0.001 HIS A 295 PHE 0.012 0.001 PHE A 34 TYR 0.016 0.001 TYR A 409 ARG 0.007 0.000 ARG A 322 Details of bonding type rmsd hydrogen bonds : bond 0.04430 ( 424) hydrogen bonds : angle 4.60572 ( 1182) covalent geometry : bond 0.00358 ( 8043) covalent geometry : angle 0.56049 (10928) Misc. bond : bond 0.00078 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 197 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 370 ASP cc_start: 0.6909 (m-30) cc_final: 0.6685 (m-30) REVERT: B 519 ARG cc_start: 0.5547 (tpt90) cc_final: 0.4689 (tpt90) REVERT: A 105 LEU cc_start: 0.8253 (mm) cc_final: 0.7972 (mp) REVERT: A 139 MET cc_start: 0.6496 (tmm) cc_final: 0.6189 (tmm) REVERT: A 209 ARG cc_start: 0.7777 (OUTLIER) cc_final: 0.7415 (mtt-85) REVERT: A 240 GLN cc_start: 0.6923 (tm-30) cc_final: 0.6626 (tm-30) REVERT: A 275 GLN cc_start: 0.7590 (pp30) cc_final: 0.7332 (pp30) REVERT: A 299 SER cc_start: 0.8430 (m) cc_final: 0.8193 (m) REVERT: A 311 GLN cc_start: 0.6811 (mt0) cc_final: 0.6561 (tt0) REVERT: A 315 MET cc_start: 0.7615 (tpp) cc_final: 0.6937 (mpp) REVERT: A 352 GLN cc_start: 0.7907 (pp30) cc_final: 0.7284 (pp30) REVERT: A 369 GLU cc_start: 0.6317 (pp20) cc_final: 0.5995 (pp20) outliers start: 40 outliers final: 21 residues processed: 220 average time/residue: 0.2274 time to fit residues: 64.9970 Evaluate side-chains 210 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 188 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 142 GLN Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 209 ARG Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 514 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 48 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 89 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 120 GLN ** B 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 HIS A 306 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.148445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.127244 restraints weight = 11900.765| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.74 r_work: 0.3469 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 8045 Z= 0.221 Angle : 0.589 7.169 10928 Z= 0.293 Chirality : 0.043 0.146 1225 Planarity : 0.005 0.043 1423 Dihedral : 5.722 54.011 1120 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 5.88 % Allowed : 26.20 % Favored : 67.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.28), residues: 984 helix: 2.09 (0.25), residues: 428 sheet: -0.01 (0.39), residues: 180 loop : 0.01 (0.36), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 391 HIS 0.008 0.001 HIS B 404 PHE 0.013 0.002 PHE A 34 TYR 0.016 0.001 TYR A 409 ARG 0.009 0.001 ARG B 466 Details of bonding type rmsd hydrogen bonds : bond 0.04393 ( 424) hydrogen bonds : angle 4.48765 ( 1182) covalent geometry : bond 0.00492 ( 8043) covalent geometry : angle 0.58950 (10928) Misc. bond : bond 0.00063 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 207 time to evaluate : 0.929 Fit side-chains revert: symmetry clash REVERT: B 139 MET cc_start: 0.8001 (tpp) cc_final: 0.7565 (ttp) REVERT: B 159 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.7047 (tt0) REVERT: B 304 ILE cc_start: 0.8523 (OUTLIER) cc_final: 0.8278 (mt) REVERT: B 370 ASP cc_start: 0.7083 (m-30) cc_final: 0.6723 (m-30) REVERT: B 519 ARG cc_start: 0.5449 (tpt90) cc_final: 0.4085 (tpt170) REVERT: A 105 LEU cc_start: 0.8315 (mm) cc_final: 0.8013 (mt) REVERT: A 158 ARG cc_start: 0.7266 (ttm-80) cc_final: 0.6976 (ttm-80) REVERT: A 209 ARG cc_start: 0.7828 (OUTLIER) cc_final: 0.7330 (mtt-85) REVERT: A 275 GLN cc_start: 0.7633 (pp30) cc_final: 0.7358 (pp30) REVERT: A 333 GLN cc_start: 0.7964 (tp-100) cc_final: 0.7706 (tp-100) REVERT: A 337 MET cc_start: 0.7557 (tpt) cc_final: 0.7333 (tpt) REVERT: A 352 GLN cc_start: 0.7990 (OUTLIER) cc_final: 0.7411 (pp30) outliers start: 50 outliers final: 33 residues processed: 233 average time/residue: 0.2243 time to fit residues: 68.3819 Evaluate side-chains 233 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 196 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 352 GLN Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 506 ASP Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 142 GLN Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 209 ARG Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 352 GLN Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 514 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 73 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 90 optimal weight: 0.3980 chunk 48 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 GLN ** B 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 GLN A 306 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.148868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.127573 restraints weight = 11881.750| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.76 r_work: 0.3473 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8045 Z= 0.189 Angle : 0.559 6.207 10928 Z= 0.279 Chirality : 0.043 0.145 1225 Planarity : 0.005 0.043 1423 Dihedral : 5.790 55.593 1120 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 6.58 % Allowed : 26.79 % Favored : 66.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.28), residues: 984 helix: 2.21 (0.25), residues: 428 sheet: 0.25 (0.40), residues: 171 loop : -0.21 (0.34), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 391 HIS 0.007 0.001 HIS B 404 PHE 0.010 0.001 PHE A 34 TYR 0.013 0.001 TYR A 409 ARG 0.007 0.000 ARG B 466 Details of bonding type rmsd hydrogen bonds : bond 0.03936 ( 424) hydrogen bonds : angle 4.30032 ( 1182) covalent geometry : bond 0.00421 ( 8043) covalent geometry : angle 0.55892 (10928) Misc. bond : bond 0.00048 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 194 time to evaluate : 0.829 Fit side-chains REVERT: B 139 MET cc_start: 0.8048 (tpp) cc_final: 0.7525 (ttp) REVERT: B 159 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.7067 (tt0) REVERT: B 304 ILE cc_start: 0.8485 (OUTLIER) cc_final: 0.8253 (mt) REVERT: B 324 ARG cc_start: 0.8161 (ttt180) cc_final: 0.7939 (ttt180) REVERT: B 337 MET cc_start: 0.7940 (tpp) cc_final: 0.7239 (tpp) REVERT: B 354 GLN cc_start: 0.8198 (tp-100) cc_final: 0.7916 (tp40) REVERT: B 370 ASP cc_start: 0.7011 (m-30) cc_final: 0.6783 (m-30) REVERT: B 519 ARG cc_start: 0.5306 (tpt90) cc_final: 0.3717 (tpt170) REVERT: A 40 GLU cc_start: 0.6780 (OUTLIER) cc_final: 0.6565 (pp20) REVERT: A 105 LEU cc_start: 0.8325 (mm) cc_final: 0.8030 (mt) REVERT: A 113 LEU cc_start: 0.7044 (OUTLIER) cc_final: 0.6740 (tt) REVERT: A 158 ARG cc_start: 0.7284 (ttm-80) cc_final: 0.6993 (ttm-80) REVERT: A 209 ARG cc_start: 0.7828 (OUTLIER) cc_final: 0.7458 (mtt-85) REVERT: A 275 GLN cc_start: 0.7627 (pp30) cc_final: 0.7318 (pp30) REVERT: A 316 GLU cc_start: 0.8010 (tt0) cc_final: 0.7802 (tp30) REVERT: A 333 GLN cc_start: 0.7973 (tp-100) cc_final: 0.7696 (tp-100) REVERT: A 337 MET cc_start: 0.7549 (tpt) cc_final: 0.7336 (tpt) REVERT: A 352 GLN cc_start: 0.7979 (OUTLIER) cc_final: 0.7420 (pp30) REVERT: A 369 GLU cc_start: 0.6354 (pp20) cc_final: 0.5819 (pp20) outliers start: 56 outliers final: 34 residues processed: 227 average time/residue: 0.2180 time to fit residues: 64.4480 Evaluate side-chains 230 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 190 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 352 GLN Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 497 ASP Chi-restraints excluded: chain B residue 506 ASP Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 209 ARG Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 352 GLN Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 514 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 27 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 16 optimal weight: 0.1980 chunk 38 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 GLN ** B 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.149004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.127788 restraints weight = 11807.971| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.76 r_work: 0.3471 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8045 Z= 0.185 Angle : 0.554 7.490 10928 Z= 0.276 Chirality : 0.042 0.165 1225 Planarity : 0.005 0.043 1423 Dihedral : 5.803 55.914 1120 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 6.11 % Allowed : 26.67 % Favored : 67.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.28), residues: 984 helix: 2.25 (0.25), residues: 429 sheet: 0.30 (0.40), residues: 166 loop : -0.26 (0.34), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 391 HIS 0.008 0.001 HIS B 404 PHE 0.010 0.001 PHE A 34 TYR 0.011 0.001 TYR A 409 ARG 0.006 0.000 ARG B 466 Details of bonding type rmsd hydrogen bonds : bond 0.03830 ( 424) hydrogen bonds : angle 4.23483 ( 1182) covalent geometry : bond 0.00413 ( 8043) covalent geometry : angle 0.55373 (10928) Misc. bond : bond 0.00041 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 200 time to evaluate : 0.973 Fit side-chains revert: symmetry clash REVERT: B 139 MET cc_start: 0.8050 (tpp) cc_final: 0.7410 (ttp) REVERT: B 159 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.7043 (tt0) REVERT: B 304 ILE cc_start: 0.8493 (OUTLIER) cc_final: 0.8261 (mt) REVERT: B 324 ARG cc_start: 0.8181 (ttt180) cc_final: 0.7971 (ttt180) REVERT: B 337 MET cc_start: 0.7941 (tpp) cc_final: 0.7229 (tpp) REVERT: B 354 GLN cc_start: 0.8216 (tp-100) cc_final: 0.7826 (tp40) REVERT: B 358 ASP cc_start: 0.7986 (m-30) cc_final: 0.7707 (m-30) REVERT: B 519 ARG cc_start: 0.5206 (tpt90) cc_final: 0.3346 (tpt170) REVERT: A 40 GLU cc_start: 0.6739 (OUTLIER) cc_final: 0.6527 (pp20) REVERT: A 79 ARG cc_start: 0.8281 (ttp-110) cc_final: 0.7896 (ttp-110) REVERT: A 105 LEU cc_start: 0.8330 (mm) cc_final: 0.8018 (mt) REVERT: A 113 LEU cc_start: 0.7046 (OUTLIER) cc_final: 0.6728 (tt) REVERT: A 158 ARG cc_start: 0.7282 (ttm-80) cc_final: 0.6991 (ttm-80) REVERT: A 209 ARG cc_start: 0.7824 (OUTLIER) cc_final: 0.7413 (mtt-85) REVERT: A 258 GLN cc_start: 0.8063 (tp40) cc_final: 0.7465 (tm-30) REVERT: A 275 GLN cc_start: 0.7638 (pp30) cc_final: 0.7310 (pp30) REVERT: A 316 GLU cc_start: 0.8017 (tt0) cc_final: 0.7808 (tp30) REVERT: A 333 GLN cc_start: 0.7982 (tp-100) cc_final: 0.7684 (tp-100) REVERT: A 369 GLU cc_start: 0.6385 (pp20) cc_final: 0.5886 (pp20) outliers start: 52 outliers final: 37 residues processed: 229 average time/residue: 0.2200 time to fit residues: 65.8592 Evaluate side-chains 235 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 193 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 352 GLN Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 506 ASP Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 142 GLN Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 209 ARG Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 514 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 71 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 41 optimal weight: 0.0570 chunk 73 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.7698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.147149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.125670 restraints weight = 11881.024| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 2.74 r_work: 0.3471 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8045 Z= 0.200 Angle : 0.563 7.694 10928 Z= 0.280 Chirality : 0.042 0.144 1225 Planarity : 0.005 0.043 1423 Dihedral : 5.848 55.678 1120 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 7.05 % Allowed : 25.85 % Favored : 67.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.28), residues: 984 helix: 2.22 (0.25), residues: 429 sheet: 0.31 (0.40), residues: 166 loop : -0.25 (0.33), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 391 HIS 0.008 0.001 HIS B 404 PHE 0.009 0.001 PHE A 34 TYR 0.010 0.001 TYR A 409 ARG 0.005 0.000 ARG B 79 Details of bonding type rmsd hydrogen bonds : bond 0.03836 ( 424) hydrogen bonds : angle 4.23310 ( 1182) covalent geometry : bond 0.00446 ( 8043) covalent geometry : angle 0.56330 (10928) Misc. bond : bond 0.00038 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 199 time to evaluate : 0.792 Fit side-chains revert: symmetry clash REVERT: B 139 MET cc_start: 0.8056 (tpp) cc_final: 0.7449 (ttp) REVERT: B 159 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.7082 (tt0) REVERT: B 304 ILE cc_start: 0.8550 (OUTLIER) cc_final: 0.8305 (mt) REVERT: B 324 ARG cc_start: 0.8200 (ttt180) cc_final: 0.7920 (ttt180) REVERT: B 337 MET cc_start: 0.7912 (tpp) cc_final: 0.7199 (tpp) REVERT: B 354 GLN cc_start: 0.8213 (tp-100) cc_final: 0.7933 (tp40) REVERT: B 519 ARG cc_start: 0.5316 (tpt90) cc_final: 0.2972 (tpt90) REVERT: B 522 ASP cc_start: 0.6880 (t0) cc_final: 0.5943 (m-30) REVERT: A 40 GLU cc_start: 0.6718 (OUTLIER) cc_final: 0.6500 (pp20) REVERT: A 79 ARG cc_start: 0.8248 (ttp-110) cc_final: 0.7985 (ttp-110) REVERT: A 105 LEU cc_start: 0.8320 (mm) cc_final: 0.8025 (mt) REVERT: A 113 LEU cc_start: 0.7066 (OUTLIER) cc_final: 0.6752 (tt) REVERT: A 158 ARG cc_start: 0.7248 (ttm-80) cc_final: 0.6963 (ttm-80) REVERT: A 209 ARG cc_start: 0.7840 (OUTLIER) cc_final: 0.7448 (mtt-85) REVERT: A 258 GLN cc_start: 0.8070 (tp40) cc_final: 0.7491 (tm-30) REVERT: A 275 GLN cc_start: 0.7632 (pp30) cc_final: 0.7292 (pp30) REVERT: A 316 GLU cc_start: 0.8045 (tt0) cc_final: 0.7839 (tp30) REVERT: A 326 THR cc_start: 0.7886 (m) cc_final: 0.7045 (p) REVERT: A 333 GLN cc_start: 0.7984 (tp-100) cc_final: 0.7670 (tp-100) REVERT: A 351 GLN cc_start: 0.7519 (OUTLIER) cc_final: 0.7260 (mp10) REVERT: A 369 GLU cc_start: 0.6381 (pp20) cc_final: 0.5935 (pp20) outliers start: 60 outliers final: 40 residues processed: 237 average time/residue: 0.2174 time to fit residues: 67.1487 Evaluate side-chains 243 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 197 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 352 GLN Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 497 ASP Chi-restraints excluded: chain B residue 506 ASP Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 209 ARG Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 351 GLN Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 514 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 34 optimal weight: 0.1980 chunk 28 optimal weight: 0.9990 chunk 90 optimal weight: 0.4980 chunk 76 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 56 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 21 optimal weight: 0.0770 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 120 GLN ** B 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.148861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.127469 restraints weight = 11961.355| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.77 r_work: 0.3497 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8045 Z= 0.132 Angle : 0.538 7.641 10928 Z= 0.265 Chirality : 0.041 0.145 1225 Planarity : 0.004 0.044 1423 Dihedral : 5.737 57.985 1120 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 5.76 % Allowed : 27.14 % Favored : 67.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.28), residues: 984 helix: 2.39 (0.25), residues: 426 sheet: 0.32 (0.40), residues: 166 loop : -0.19 (0.34), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 391 HIS 0.006 0.001 HIS B 404 PHE 0.008 0.001 PHE A 199 TYR 0.012 0.001 TYR A 409 ARG 0.011 0.000 ARG B 466 Details of bonding type rmsd hydrogen bonds : bond 0.03379 ( 424) hydrogen bonds : angle 4.11653 ( 1182) covalent geometry : bond 0.00295 ( 8043) covalent geometry : angle 0.53817 (10928) Misc. bond : bond 0.00034 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 200 time to evaluate : 0.891 Fit side-chains revert: symmetry clash REVERT: B 139 MET cc_start: 0.8037 (tpp) cc_final: 0.7379 (ttp) REVERT: B 159 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.7012 (tt0) REVERT: B 203 ASP cc_start: 0.7173 (m-30) cc_final: 0.6909 (t0) REVERT: B 337 MET cc_start: 0.7901 (tpp) cc_final: 0.7177 (tpp) REVERT: B 354 GLN cc_start: 0.8176 (tp-100) cc_final: 0.7907 (tp40) REVERT: B 519 ARG cc_start: 0.5132 (tpt90) cc_final: 0.2735 (tpt90) REVERT: A 40 GLU cc_start: 0.6605 (OUTLIER) cc_final: 0.6230 (pp20) REVERT: A 79 ARG cc_start: 0.8261 (ttp-110) cc_final: 0.7884 (ttp-110) REVERT: A 105 LEU cc_start: 0.8269 (mm) cc_final: 0.7970 (mt) REVERT: A 113 LEU cc_start: 0.7034 (OUTLIER) cc_final: 0.6704 (tt) REVERT: A 143 LEU cc_start: 0.7783 (mt) cc_final: 0.7198 (mp) REVERT: A 258 GLN cc_start: 0.8012 (tp40) cc_final: 0.7428 (tm-30) REVERT: A 275 GLN cc_start: 0.7627 (pp30) cc_final: 0.7276 (pp30) REVERT: A 316 GLU cc_start: 0.8018 (tt0) cc_final: 0.7806 (tp30) REVERT: A 326 THR cc_start: 0.7918 (m) cc_final: 0.6992 (p) REVERT: A 333 GLN cc_start: 0.7981 (tp-100) cc_final: 0.7664 (tp-100) REVERT: A 351 GLN cc_start: 0.7408 (OUTLIER) cc_final: 0.7145 (mp10) REVERT: A 355 LEU cc_start: 0.7978 (mt) cc_final: 0.7747 (mt) REVERT: A 369 GLU cc_start: 0.6352 (pp20) cc_final: 0.5904 (pp20) REVERT: A 406 SER cc_start: 0.7643 (OUTLIER) cc_final: 0.6527 (p) outliers start: 49 outliers final: 32 residues processed: 229 average time/residue: 0.2208 time to fit residues: 66.3153 Evaluate side-chains 232 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 195 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 352 GLN Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 497 ASP Chi-restraints excluded: chain B residue 506 ASP Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 351 GLN Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 514 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 23 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 24 optimal weight: 0.0270 chunk 5 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 58 optimal weight: 0.0000 chunk 88 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 87 optimal weight: 0.4980 chunk 49 optimal weight: 0.0170 chunk 26 optimal weight: 0.8980 overall best weight: 0.2480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 HIS B 120 GLN ** B 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 HIS A 302 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.150688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.129202 restraints weight = 11997.729| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 2.79 r_work: 0.3526 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8045 Z= 0.104 Angle : 0.526 7.949 10928 Z= 0.258 Chirality : 0.041 0.156 1225 Planarity : 0.004 0.045 1423 Dihedral : 5.593 59.634 1120 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 4.58 % Allowed : 27.73 % Favored : 67.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.28), residues: 984 helix: 2.48 (0.25), residues: 427 sheet: 0.25 (0.40), residues: 165 loop : -0.15 (0.34), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 391 HIS 0.004 0.001 HIS B 404 PHE 0.007 0.001 PHE A 199 TYR 0.020 0.001 TYR A 409 ARG 0.009 0.000 ARG B 466 Details of bonding type rmsd hydrogen bonds : bond 0.03105 ( 424) hydrogen bonds : angle 3.99080 ( 1182) covalent geometry : bond 0.00233 ( 8043) covalent geometry : angle 0.52560 (10928) Misc. bond : bond 0.00029 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 200 time to evaluate : 0.828 Fit side-chains revert: symmetry clash REVERT: B 139 MET cc_start: 0.7997 (tpp) cc_final: 0.7345 (ttp) REVERT: B 159 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.6990 (tt0) REVERT: B 203 ASP cc_start: 0.7168 (m-30) cc_final: 0.6896 (t0) REVERT: B 337 MET cc_start: 0.7852 (tpp) cc_final: 0.7139 (tpp) REVERT: B 354 GLN cc_start: 0.8196 (tp-100) cc_final: 0.7946 (tp40) REVERT: B 519 ARG cc_start: 0.4878 (tpt90) cc_final: 0.2554 (tpt90) REVERT: A 40 GLU cc_start: 0.6526 (OUTLIER) cc_final: 0.6150 (pp20) REVERT: A 105 LEU cc_start: 0.8198 (mm) cc_final: 0.7908 (mp) REVERT: A 113 LEU cc_start: 0.7011 (OUTLIER) cc_final: 0.6682 (tt) REVERT: A 143 LEU cc_start: 0.7662 (mt) cc_final: 0.7235 (mp) REVERT: A 209 ARG cc_start: 0.7788 (OUTLIER) cc_final: 0.7573 (mtt-85) REVERT: A 240 GLN cc_start: 0.6894 (tm-30) cc_final: 0.6504 (tm-30) REVERT: A 258 GLN cc_start: 0.7971 (tp40) cc_final: 0.7372 (tm-30) REVERT: A 275 GLN cc_start: 0.7623 (pp30) cc_final: 0.7261 (pp30) REVERT: A 316 GLU cc_start: 0.8000 (tt0) cc_final: 0.7768 (tp30) REVERT: A 326 THR cc_start: 0.7863 (m) cc_final: 0.6973 (p) REVERT: A 333 GLN cc_start: 0.8001 (tp-100) cc_final: 0.7699 (tp-100) REVERT: A 355 LEU cc_start: 0.7979 (mt) cc_final: 0.7748 (mt) REVERT: A 369 GLU cc_start: 0.6332 (pp20) cc_final: 0.5889 (pp20) REVERT: A 406 SER cc_start: 0.7593 (OUTLIER) cc_final: 0.6575 (p) REVERT: A 500 ARG cc_start: 0.7969 (ttp-170) cc_final: 0.7496 (ttp-170) outliers start: 39 outliers final: 24 residues processed: 226 average time/residue: 0.2165 time to fit residues: 64.0245 Evaluate side-chains 222 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 193 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 120 GLN Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 352 GLN Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 209 ARG Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 514 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 34 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 89 optimal weight: 0.0570 chunk 81 optimal weight: 0.7980 chunk 47 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 HIS ** 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 = 0.3931 r_free = 0.3931 target = 0.148758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.126914 restraints weight = 12175.148| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 2.82 r_work: 0.3496 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8045 Z= 0.151 Angle : 0.550 7.661 10928 Z= 0.271 Chirality : 0.042 0.149 1225 Planarity : 0.005 0.044 1423 Dihedral : 5.693 57.351 1120 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.88 % Allowed : 28.79 % Favored : 67.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.28), residues: 984 helix: 2.40 (0.25), residues: 427 sheet: 0.29 (0.39), residues: 166 loop : -0.11 (0.35), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 391 HIS 0.006 0.001 HIS B 404 PHE 0.009 0.001 PHE A 34 TYR 0.021 0.001 TYR A 409 ARG 0.010 0.001 ARG B 466 Details of bonding type rmsd hydrogen bonds : bond 0.03381 ( 424) hydrogen bonds : angle 4.04448 ( 1182) covalent geometry : bond 0.00343 ( 8043) covalent geometry : angle 0.55007 (10928) Misc. bond : bond 0.00030 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 192 time to evaluate : 0.798 Fit side-chains revert: symmetry clash REVERT: B 139 MET cc_start: 0.8001 (tpp) cc_final: 0.7333 (ttp) REVERT: B 159 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.7045 (tt0) REVERT: B 203 ASP cc_start: 0.7193 (m-30) cc_final: 0.6931 (t0) REVERT: B 304 ILE cc_start: 0.8470 (OUTLIER) cc_final: 0.8076 (tt) REVERT: B 337 MET cc_start: 0.7889 (tpp) cc_final: 0.7144 (tpp) REVERT: B 354 GLN cc_start: 0.8200 (tp-100) cc_final: 0.7934 (tp40) REVERT: B 519 ARG cc_start: 0.5057 (tpt90) cc_final: 0.2601 (tpt90) REVERT: B 522 ASP cc_start: 0.6933 (t0) cc_final: 0.6024 (m-30) REVERT: A 40 GLU cc_start: 0.6587 (OUTLIER) cc_final: 0.6371 (pp20) REVERT: A 79 ARG cc_start: 0.8300 (ttp-110) cc_final: 0.7947 (ttp-110) REVERT: A 105 LEU cc_start: 0.8268 (mm) cc_final: 0.7966 (mt) REVERT: A 113 LEU cc_start: 0.7081 (OUTLIER) cc_final: 0.6777 (tt) REVERT: A 143 LEU cc_start: 0.7686 (mt) cc_final: 0.7276 (mp) REVERT: A 209 ARG cc_start: 0.7812 (OUTLIER) cc_final: 0.7457 (mtt-85) REVERT: A 275 GLN cc_start: 0.7645 (pp30) cc_final: 0.7282 (pp30) REVERT: A 316 GLU cc_start: 0.7999 (tt0) cc_final: 0.7755 (tp30) REVERT: A 326 THR cc_start: 0.7870 (m) cc_final: 0.6996 (p) REVERT: A 333 GLN cc_start: 0.8015 (tp-100) cc_final: 0.7808 (tp-100) REVERT: A 355 LEU cc_start: 0.8061 (mt) cc_final: 0.7785 (mt) REVERT: A 369 GLU cc_start: 0.6405 (pp20) cc_final: 0.5944 (pp20) REVERT: A 406 SER cc_start: 0.7619 (OUTLIER) cc_final: 0.6634 (p) outliers start: 33 outliers final: 27 residues processed: 215 average time/residue: 0.2284 time to fit residues: 64.2067 Evaluate side-chains 223 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 190 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 352 GLN Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 142 GLN Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 209 ARG Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 514 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 54 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 14 optimal weight: 0.0030 chunk 13 optimal weight: 0.9990 chunk 88 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 91 optimal weight: 0.4980 chunk 3 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 120 GLN ** B 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.148997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.127388 restraints weight = 12028.214| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.79 r_work: 0.3500 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8045 Z= 0.146 Angle : 0.558 7.875 10928 Z= 0.274 Chirality : 0.042 0.153 1225 Planarity : 0.005 0.043 1423 Dihedral : 5.805 57.245 1120 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 4.11 % Allowed : 28.32 % Favored : 67.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.28), residues: 984 helix: 2.39 (0.25), residues: 425 sheet: 0.26 (0.39), residues: 166 loop : -0.07 (0.35), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 391 HIS 0.006 0.001 HIS B 404 PHE 0.009 0.001 PHE A 34 TYR 0.021 0.001 TYR A 409 ARG 0.010 0.001 ARG B 466 Details of bonding type rmsd hydrogen bonds : bond 0.03385 ( 424) hydrogen bonds : angle 4.06488 ( 1182) covalent geometry : bond 0.00331 ( 8043) covalent geometry : angle 0.55790 (10928) Misc. bond : bond 0.00029 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 192 time to evaluate : 0.858 Fit side-chains revert: symmetry clash REVERT: B 79 ARG cc_start: 0.8389 (ttm110) cc_final: 0.7979 (ptp-110) REVERT: B 139 MET cc_start: 0.7979 (tpp) cc_final: 0.7302 (ttp) REVERT: B 159 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.7036 (tt0) REVERT: B 203 ASP cc_start: 0.7193 (m-30) cc_final: 0.6932 (t0) REVERT: B 304 ILE cc_start: 0.8463 (OUTLIER) cc_final: 0.8070 (tt) REVERT: B 337 MET cc_start: 0.7885 (tpp) cc_final: 0.7124 (tpp) REVERT: B 354 GLN cc_start: 0.8178 (tp-100) cc_final: 0.7906 (tp40) REVERT: B 368 ILE cc_start: 0.8124 (OUTLIER) cc_final: 0.7913 (tp) REVERT: B 519 ARG cc_start: 0.5075 (tpt90) cc_final: 0.2590 (tpt90) REVERT: B 522 ASP cc_start: 0.6955 (t0) cc_final: 0.5985 (m-30) REVERT: A 40 GLU cc_start: 0.6602 (OUTLIER) cc_final: 0.6236 (pp20) REVERT: A 79 ARG cc_start: 0.8300 (ttp-110) cc_final: 0.7944 (ttp-110) REVERT: A 105 LEU cc_start: 0.8259 (mm) cc_final: 0.7957 (mt) REVERT: A 113 LEU cc_start: 0.7079 (OUTLIER) cc_final: 0.6779 (tt) REVERT: A 143 LEU cc_start: 0.7701 (mt) cc_final: 0.7299 (mp) REVERT: A 209 ARG cc_start: 0.7809 (OUTLIER) cc_final: 0.7590 (mtt-85) REVERT: A 258 GLN cc_start: 0.8009 (tp40) cc_final: 0.7391 (tm-30) REVERT: A 275 GLN cc_start: 0.7637 (pp30) cc_final: 0.7273 (pp30) REVERT: A 316 GLU cc_start: 0.7989 (tt0) cc_final: 0.7747 (tp30) REVERT: A 326 THR cc_start: 0.7862 (m) cc_final: 0.6979 (p) REVERT: A 333 GLN cc_start: 0.8019 (tp-100) cc_final: 0.7765 (tp-100) REVERT: A 355 LEU cc_start: 0.8025 (mt) cc_final: 0.7778 (mt) REVERT: A 369 GLU cc_start: 0.6394 (pp20) cc_final: 0.5940 (pp20) REVERT: A 391 TRP cc_start: 0.7485 (t60) cc_final: 0.7147 (t60) REVERT: A 406 SER cc_start: 0.7623 (OUTLIER) cc_final: 0.6634 (p) outliers start: 35 outliers final: 28 residues processed: 216 average time/residue: 0.2192 time to fit residues: 62.2296 Evaluate side-chains 226 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 191 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 120 GLN Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 352 GLN Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 142 GLN Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 209 ARG Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 514 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 24 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 65 optimal weight: 0.5980 chunk 66 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 6 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 120 GLN ** B 179 HIS ** 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 = 0.3918 r_free = 0.3918 target = 0.147800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.126040 restraints weight = 11929.353| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.78 r_work: 0.3473 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8045 Z= 0.199 Angle : 0.586 7.828 10928 Z= 0.291 Chirality : 0.043 0.148 1225 Planarity : 0.005 0.044 1423 Dihedral : 5.916 55.595 1120 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 4.70 % Allowed : 27.73 % Favored : 67.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.28), residues: 984 helix: 2.27 (0.25), residues: 425 sheet: 0.28 (0.40), residues: 166 loop : -0.09 (0.34), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 391 HIS 0.006 0.001 HIS B 404 PHE 0.011 0.001 PHE A 34 TYR 0.021 0.001 TYR A 409 ARG 0.010 0.001 ARG B 466 Details of bonding type rmsd hydrogen bonds : bond 0.03668 ( 424) hydrogen bonds : angle 4.13483 ( 1182) covalent geometry : bond 0.00449 ( 8043) covalent geometry : angle 0.58585 (10928) Misc. bond : bond 0.00033 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4498.42 seconds wall clock time: 78 minutes 31.32 seconds (4711.32 seconds total)