Starting phenix.real_space_refine on Tue Jul 29 22:33:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jlo_22375/07_2025/7jlo_22375.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jlo_22375/07_2025/7jlo_22375.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7jlo_22375/07_2025/7jlo_22375.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jlo_22375/07_2025/7jlo_22375.map" model { file = "/net/cci-nas-00/data/ceres_data/7jlo_22375/07_2025/7jlo_22375.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jlo_22375/07_2025/7jlo_22375.cif" } resolution = 3.4 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= 0.009 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 69 5.16 5 C 7881 2.51 5 N 2022 2.21 5 O 1992 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 87 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11964 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3988 Classifications: {'peptide': 485} Link IDs: {'PTRANS': 18, 'TRANS': 466} Chain breaks: 1 Restraints were copied for chains: C, B Time building chain proxies: 8.32, per 1000 atoms: 0.70 Number of scatterers: 11964 At special positions: 0 Unit cell: (129.276, 123.606, 88.452, 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 69 16.00 O 1992 8.00 N 2022 7.00 C 7881 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 86 " - pdb=" SG CYS A 122 " distance=2.04 Simple disulfide: pdb=" SG CYS C 86 " - pdb=" SG CYS C 122 " distance=2.04 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 122 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.68 Conformation dependent library (CDL) restraints added in 1.5 seconds 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2772 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 9 sheets defined 72.0% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.92 Creating SS restraints... Processing helix chain 'A' and resid 42 through 56 Processing helix chain 'A' and resid 58 through 86 Processing helix chain 'A' and resid 111 through 116 removed outlier: 3.934A pdb=" N ALA A 115 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 111 through 116' Processing helix chain 'A' and resid 118 through 128 Processing helix chain 'A' and resid 130 through 168 removed outlier: 4.045A pdb=" N ILE A 135 " --> pdb=" O SER A 131 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N CYS A 155 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE A 160 " --> pdb=" O CYS A 156 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 168 " --> pdb=" O TYR A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 190 Processing helix chain 'A' and resid 204 through 213 Processing helix chain 'A' and resid 213 through 226 removed outlier: 3.746A pdb=" N TYR A 218 " --> pdb=" O ARG A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 256 Processing helix chain 'A' and resid 270 through 275 removed outlier: 3.667A pdb=" N ARG A 275 " --> pdb=" O GLU A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 300 Processing helix chain 'A' and resid 300 through 317 removed outlier: 3.612A pdb=" N ALA A 317 " --> pdb=" O PHE A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 323 Processing helix chain 'A' and resid 324 through 328 removed outlier: 4.270A pdb=" N LEU A 327 " --> pdb=" O PRO A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 340 removed outlier: 3.591A pdb=" N CYS A 338 " --> pdb=" O LEU A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 357 removed outlier: 3.881A pdb=" N ARG A 353 " --> pdb=" O GLU A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 367 removed outlier: 3.559A pdb=" N MET A 365 " --> pdb=" O ALA A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 398 removed outlier: 3.605A pdb=" N VAL A 390 " --> pdb=" O SER A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 404 Processing helix chain 'A' and resid 406 through 422 Processing helix chain 'A' and resid 433 through 446 removed outlier: 3.581A pdb=" N LEU A 437 " --> pdb=" O CYS A 433 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU A 438 " --> pdb=" O PRO A 434 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG A 439 " --> pdb=" O GLU A 435 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL A 440 " --> pdb=" O GLN A 436 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA A 443 " --> pdb=" O ARG A 439 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N HIS A 444 " --> pdb=" O VAL A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 453 removed outlier: 3.525A pdb=" N TRP A 452 " --> pdb=" O PRO A 449 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLN A 453 " --> pdb=" O ASP A 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 449 through 453' Processing helix chain 'A' and resid 460 through 466 Processing helix chain 'A' and resid 472 through 481 Processing helix chain 'A' and resid 481 through 492 Proline residue: A 487 - end of helix Processing helix chain 'A' and resid 497 through 508 removed outlier: 3.785A pdb=" N ILE A 502 " --> pdb=" O ALA A 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 56 Processing helix chain 'B' and resid 58 through 86 Processing helix chain 'B' and resid 111 through 116 removed outlier: 3.935A pdb=" N ALA B 115 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE B 116 " --> pdb=" O LEU B 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 111 through 116' Processing helix chain 'B' and resid 118 through 128 Processing helix chain 'B' and resid 130 through 168 removed outlier: 4.045A pdb=" N ILE B 135 " --> pdb=" O SER B 131 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N CYS B 155 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILE B 160 " --> pdb=" O CYS B 156 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU B 168 " --> pdb=" O TYR B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 190 Processing helix chain 'B' and resid 204 through 213 Processing helix chain 'B' and resid 213 through 226 removed outlier: 3.746A pdb=" N TYR B 218 " --> pdb=" O ARG B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 256 Processing helix chain 'B' and resid 270 through 275 removed outlier: 3.667A pdb=" N ARG B 275 " --> pdb=" O GLU B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 300 Processing helix chain 'B' and resid 300 through 317 removed outlier: 3.612A pdb=" N ALA B 317 " --> pdb=" O PHE B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 323 Processing helix chain 'B' and resid 324 through 328 removed outlier: 4.270A pdb=" N LEU B 327 " --> pdb=" O PRO B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 340 removed outlier: 3.591A pdb=" N CYS B 338 " --> pdb=" O LEU B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 357 removed outlier: 3.880A pdb=" N ARG B 353 " --> pdb=" O GLU B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 367 removed outlier: 3.558A pdb=" N MET B 365 " --> pdb=" O ALA B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 398 removed outlier: 3.605A pdb=" N VAL B 390 " --> pdb=" O SER B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 404 Processing helix chain 'B' and resid 406 through 422 Processing helix chain 'B' and resid 433 through 446 removed outlier: 3.581A pdb=" N LEU B 437 " --> pdb=" O CYS B 433 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU B 438 " --> pdb=" O PRO B 434 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG B 439 " --> pdb=" O GLU B 435 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL B 440 " --> pdb=" O GLN B 436 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA B 443 " --> pdb=" O ARG B 439 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N HIS B 444 " --> pdb=" O VAL B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 453 removed outlier: 3.525A pdb=" N TRP B 452 " --> pdb=" O PRO B 449 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLN B 453 " --> pdb=" O ASP B 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 449 through 453' Processing helix chain 'B' and resid 460 through 466 Processing helix chain 'B' and resid 472 through 481 Processing helix chain 'B' and resid 481 through 492 Proline residue: B 487 - end of helix Processing helix chain 'B' and resid 497 through 508 removed outlier: 3.785A pdb=" N ILE B 502 " --> pdb=" O ALA B 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 56 Processing helix chain 'C' and resid 58 through 86 Processing helix chain 'C' and resid 111 through 116 removed outlier: 3.933A pdb=" N ALA C 115 " --> pdb=" O THR C 111 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE C 116 " --> pdb=" O LEU C 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 111 through 116' Processing helix chain 'C' and resid 118 through 128 Processing helix chain 'C' and resid 130 through 168 removed outlier: 4.045A pdb=" N ILE C 135 " --> pdb=" O SER C 131 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N CYS C 155 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE C 160 " --> pdb=" O CYS C 156 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU C 168 " --> pdb=" O TYR C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 190 Processing helix chain 'C' and resid 204 through 213 Processing helix chain 'C' and resid 213 through 226 removed outlier: 3.746A pdb=" N TYR C 218 " --> pdb=" O ARG C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 256 Processing helix chain 'C' and resid 270 through 275 removed outlier: 3.667A pdb=" N ARG C 275 " --> pdb=" O GLU C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 300 Processing helix chain 'C' and resid 300 through 317 removed outlier: 3.612A pdb=" N ALA C 317 " --> pdb=" O PHE C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 323 Processing helix chain 'C' and resid 324 through 328 removed outlier: 4.270A pdb=" N LEU C 327 " --> pdb=" O PRO C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 340 removed outlier: 3.590A pdb=" N CYS C 338 " --> pdb=" O LEU C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 357 removed outlier: 3.881A pdb=" N ARG C 353 " --> pdb=" O GLU C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 367 removed outlier: 3.558A pdb=" N MET C 365 " --> pdb=" O ALA C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 398 removed outlier: 3.605A pdb=" N VAL C 390 " --> pdb=" O SER C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 404 Processing helix chain 'C' and resid 406 through 422 Processing helix chain 'C' and resid 433 through 446 removed outlier: 3.581A pdb=" N LEU C 437 " --> pdb=" O CYS C 433 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LEU C 438 " --> pdb=" O PRO C 434 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG C 439 " --> pdb=" O GLU C 435 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL C 440 " --> pdb=" O GLN C 436 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA C 443 " --> pdb=" O ARG C 439 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N HIS C 444 " --> pdb=" O VAL C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 453 removed outlier: 3.524A pdb=" N TRP C 452 " --> pdb=" O PRO C 449 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLN C 453 " --> pdb=" O ASP C 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 449 through 453' Processing helix chain 'C' and resid 460 through 466 Processing helix chain 'C' and resid 472 through 481 Processing helix chain 'C' and resid 481 through 492 Proline residue: C 487 - end of helix Processing helix chain 'C' and resid 497 through 508 removed outlier: 3.785A pdb=" N ILE C 502 " --> pdb=" O ALA C 498 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 231 through 234 Processing sheet with id=AA2, first strand: chain 'A' and resid 330 through 332 Processing sheet with id=AA3, first strand: chain 'A' and resid 509 through 512 Processing sheet with id=AA4, first strand: chain 'B' and resid 231 through 234 Processing sheet with id=AA5, first strand: chain 'B' and resid 330 through 332 Processing sheet with id=AA6, first strand: chain 'B' and resid 509 through 512 Processing sheet with id=AA7, first strand: chain 'C' and resid 231 through 234 Processing sheet with id=AA8, first strand: chain 'C' and resid 330 through 332 Processing sheet with id=AA9, first strand: chain 'C' and resid 509 through 512 699 hydrogen bonds defined for protein. 2025 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: 4.41 Time building geometry restraints manager: 3.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3759 1.34 - 1.46: 3117 1.46 - 1.58: 5331 1.58 - 1.70: 0 1.70 - 1.82: 93 Bond restraints: 12300 Sorted by residual: bond pdb=" C HIS A 451 " pdb=" N TRP A 452 " ideal model delta sigma weight residual 1.332 1.318 0.015 1.40e-02 5.10e+03 1.12e+00 bond pdb=" C HIS B 451 " pdb=" N TRP B 452 " ideal model delta sigma weight residual 1.332 1.318 0.014 1.40e-02 5.10e+03 1.01e+00 bond pdb=" C HIS C 451 " pdb=" N TRP C 452 " ideal model delta sigma weight residual 1.332 1.319 0.014 1.40e-02 5.10e+03 9.82e-01 bond pdb=" C TYR C 152 " pdb=" O TYR C 152 " ideal model delta sigma weight residual 1.236 1.246 -0.010 1.15e-02 7.56e+03 7.45e-01 bond pdb=" CB GLU C 399 " pdb=" CG GLU C 399 " ideal model delta sigma weight residual 1.520 1.495 0.025 3.00e-02 1.11e+03 7.21e-01 ... (remaining 12295 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.07: 15593 1.07 - 2.14: 937 2.14 - 3.21: 114 3.21 - 4.28: 39 4.28 - 5.35: 24 Bond angle restraints: 16707 Sorted by residual: angle pdb=" N GLN C 528 " pdb=" CA GLN C 528 " pdb=" C GLN C 528 " ideal model delta sigma weight residual 111.02 115.45 -4.43 1.22e+00 6.72e-01 1.32e+01 angle pdb=" N GLN B 528 " pdb=" CA GLN B 528 " pdb=" C GLN B 528 " ideal model delta sigma weight residual 111.02 115.42 -4.40 1.22e+00 6.72e-01 1.30e+01 angle pdb=" N GLN A 528 " pdb=" CA GLN A 528 " pdb=" C GLN A 528 " ideal model delta sigma weight residual 111.02 115.42 -4.40 1.22e+00 6.72e-01 1.30e+01 angle pdb=" N ARG C 527 " pdb=" CA ARG C 527 " pdb=" C ARG C 527 " ideal model delta sigma weight residual 109.96 105.28 4.68 1.68e+00 3.54e-01 7.77e+00 angle pdb=" N ARG B 527 " pdb=" CA ARG B 527 " pdb=" C ARG B 527 " ideal model delta sigma weight residual 109.96 105.30 4.66 1.68e+00 3.54e-01 7.69e+00 ... (remaining 16702 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 6455 17.83 - 35.67: 573 35.67 - 53.50: 112 53.50 - 71.33: 30 71.33 - 89.17: 12 Dihedral angle restraints: 7182 sinusoidal: 2904 harmonic: 4278 Sorted by residual: dihedral pdb=" CA ARG B 527 " pdb=" C ARG B 527 " pdb=" N GLN B 528 " pdb=" CA GLN B 528 " ideal model delta harmonic sigma weight residual -180.00 -159.72 -20.28 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA ARG A 527 " pdb=" C ARG A 527 " pdb=" N GLN A 528 " pdb=" CA GLN A 528 " ideal model delta harmonic sigma weight residual -180.00 -159.72 -20.28 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA ARG C 527 " pdb=" C ARG C 527 " pdb=" N GLN C 528 " pdb=" CA GLN C 528 " ideal model delta harmonic sigma weight residual -180.00 -159.73 -20.27 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 7179 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 846 0.024 - 0.047: 542 0.047 - 0.071: 328 0.071 - 0.095: 86 0.095 - 0.118: 67 Chirality restraints: 1869 Sorted by residual: chirality pdb=" CA ILE C 170 " pdb=" N ILE C 170 " pdb=" C ILE C 170 " pdb=" CB ILE C 170 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.50e-01 chirality pdb=" CA ILE A 170 " pdb=" N ILE A 170 " pdb=" C ILE A 170 " pdb=" CB ILE A 170 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.48e-01 chirality pdb=" CA ILE B 170 " pdb=" N ILE B 170 " pdb=" C ILE B 170 " pdb=" CB ILE B 170 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.45e-01 ... (remaining 1866 not shown) Planarity restraints: 2085 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 117 " 0.020 5.00e-02 4.00e+02 3.10e-02 1.54e+00 pdb=" N PRO B 118 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO B 118 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 118 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 117 " 0.020 5.00e-02 4.00e+02 3.09e-02 1.53e+00 pdb=" N PRO C 118 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO C 118 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 118 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 117 " -0.020 5.00e-02 4.00e+02 3.08e-02 1.52e+00 pdb=" N PRO A 118 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 118 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 118 " -0.017 5.00e-02 4.00e+02 ... (remaining 2082 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1152 2.74 - 3.28: 11901 3.28 - 3.82: 19337 3.82 - 4.36: 22439 4.36 - 4.90: 39499 Nonbonded interactions: 94328 Sorted by model distance: nonbonded pdb=" O HIS C 406 " pdb=" OG1 THR C 410 " model vdw 2.203 3.040 nonbonded pdb=" O HIS B 406 " pdb=" OG1 THR B 410 " model vdw 2.203 3.040 nonbonded pdb=" O HIS A 406 " pdb=" OG1 THR A 410 " model vdw 2.203 3.040 nonbonded pdb=" NH2 ARG B 337 " pdb=" OE1 GLN B 351 " model vdw 2.230 3.120 nonbonded pdb=" NH2 ARG A 337 " pdb=" OE1 GLN A 351 " model vdw 2.231 3.120 ... (remaining 94323 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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: 0.510 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: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.110 Process input model: 31.170 Find NCS groups from input model: 0.230 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: 0.010 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 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 : 0.004 0.031 12303 Z= 0.198 Angle : 0.604 5.350 16713 Z= 0.361 Chirality : 0.041 0.118 1869 Planarity : 0.003 0.031 2085 Dihedral : 14.679 89.167 4401 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.46 % Allowed : 5.03 % Favored : 94.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.20), residues: 1443 helix: -0.55 (0.16), residues: 954 sheet: None (None), residues: 0 loop : -3.14 (0.21), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 180 HIS 0.003 0.001 HIS C 161 PHE 0.018 0.001 PHE C 79 TYR 0.012 0.001 TYR B 152 ARG 0.002 0.000 ARG A 495 Details of bonding type rmsd hydrogen bonds : bond 0.11522 ( 699) hydrogen bonds : angle 5.04083 ( 2025) SS BOND : bond 0.00582 ( 3) SS BOND : angle 1.67656 ( 6) covalent geometry : bond 0.00443 (12300) covalent geometry : angle 0.60289 (16707) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 206 time to evaluate : 1.253 Fit side-chains REVERT: A 62 MET cc_start: 0.8289 (ttp) cc_final: 0.7877 (ttp) REVERT: A 69 GLU cc_start: 0.7625 (mm-30) cc_final: 0.7350 (mm-30) REVERT: A 422 ARG cc_start: 0.7615 (tpt-90) cc_final: 0.7265 (mmm160) REVERT: B 69 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7668 (mm-30) REVERT: B 125 ARG cc_start: 0.8289 (ttm-80) cc_final: 0.8004 (ttm110) REVERT: B 159 GLU cc_start: 0.8039 (tm-30) cc_final: 0.7755 (tm-30) REVERT: B 372 LEU cc_start: 0.8587 (tp) cc_final: 0.8378 (tp) REVERT: B 427 ASP cc_start: 0.8598 (p0) cc_final: 0.8355 (p0) REVERT: C 89 TYR cc_start: 0.8861 (m-80) cc_final: 0.8585 (m-80) outliers start: 6 outliers final: 2 residues processed: 209 average time/residue: 0.2964 time to fit residues: 82.8144 Evaluate side-chains 133 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 131 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain B residue 137 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 112 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 130 optimal weight: 0.7980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 HIS A 342 HIS A 467 GLN ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 HIS B 342 HIS B 428 GLN B 451 HIS B 467 GLN ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 GLN C 210 HIS C 342 HIS C 467 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.123857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.100435 restraints weight = 16080.688| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 1.79 r_work: 0.2865 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 12303 Z= 0.115 Angle : 0.495 5.266 16713 Z= 0.259 Chirality : 0.038 0.120 1869 Planarity : 0.004 0.057 2085 Dihedral : 4.425 22.930 1595 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.62 % Allowed : 11.14 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.22), residues: 1443 helix: 0.81 (0.18), residues: 936 sheet: -1.28 (0.84), residues: 30 loop : -2.51 (0.23), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 180 HIS 0.003 0.001 HIS A 161 PHE 0.010 0.001 PHE B 79 TYR 0.017 0.001 TYR A 152 ARG 0.006 0.000 ARG A 125 Details of bonding type rmsd hydrogen bonds : bond 0.04340 ( 699) hydrogen bonds : angle 3.75387 ( 2025) SS BOND : bond 0.00015 ( 3) SS BOND : angle 1.05953 ( 6) covalent geometry : bond 0.00257 (12300) covalent geometry : angle 0.49418 (16707) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 135 time to evaluate : 1.261 Fit side-chains REVERT: A 62 MET cc_start: 0.8585 (ttp) cc_final: 0.8339 (ttp) REVERT: A 69 GLU cc_start: 0.8636 (mm-30) cc_final: 0.8408 (mm-30) REVERT: A 300 LEU cc_start: 0.8499 (mm) cc_final: 0.8242 (mt) REVERT: A 422 ARG cc_start: 0.8327 (tpt-90) cc_final: 0.8000 (mmp80) REVERT: B 51 TYR cc_start: 0.9406 (t80) cc_final: 0.8718 (t80) REVERT: B 69 GLU cc_start: 0.8699 (mm-30) cc_final: 0.8488 (mm-30) REVERT: B 125 ARG cc_start: 0.8475 (ttm-80) cc_final: 0.7947 (ttm110) REVERT: B 146 ARG cc_start: 0.8521 (mtm180) cc_final: 0.8234 (mtm110) REVERT: B 159 GLU cc_start: 0.8593 (tm-30) cc_final: 0.8183 (tm-30) REVERT: B 396 ILE cc_start: 0.8627 (mt) cc_final: 0.8385 (mm) REVERT: B 422 ARG cc_start: 0.8339 (mmm160) cc_final: 0.7647 (mmp80) REVERT: C 159 GLU cc_start: 0.8463 (tm-30) cc_final: 0.7978 (tm-30) outliers start: 8 outliers final: 5 residues processed: 140 average time/residue: 0.2934 time to fit residues: 56.3366 Evaluate side-chains 121 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 116 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 431 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 106 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 60 optimal weight: 6.9990 chunk 47 optimal weight: 10.0000 chunk 111 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 chunk 88 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 HIS ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 GLN B 379 ASN ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 451 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.120884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.097535 restraints weight = 16490.961| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 1.77 r_work: 0.2808 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 12303 Z= 0.180 Angle : 0.530 7.042 16713 Z= 0.275 Chirality : 0.040 0.188 1869 Planarity : 0.004 0.033 2085 Dihedral : 4.491 22.989 1593 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.70 % Allowed : 12.84 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.22), residues: 1443 helix: 0.92 (0.18), residues: 957 sheet: -1.19 (0.87), residues: 30 loop : -2.18 (0.24), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 180 HIS 0.003 0.001 HIS C 348 PHE 0.015 0.001 PHE B 79 TYR 0.016 0.001 TYR A 152 ARG 0.003 0.000 ARG A 146 Details of bonding type rmsd hydrogen bonds : bond 0.04973 ( 699) hydrogen bonds : angle 3.80972 ( 2025) SS BOND : bond 0.00152 ( 3) SS BOND : angle 0.92142 ( 6) covalent geometry : bond 0.00436 (12300) covalent geometry : angle 0.52999 (16707) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 1.249 Fit side-chains REVERT: A 422 ARG cc_start: 0.8374 (tpt-90) cc_final: 0.8098 (mmp80) REVERT: B 125 ARG cc_start: 0.8508 (ttm-80) cc_final: 0.7964 (ttm110) REVERT: B 146 ARG cc_start: 0.8519 (mtm180) cc_final: 0.8183 (mtm110) REVERT: B 159 GLU cc_start: 0.8661 (tm-30) cc_final: 0.8304 (tm-30) REVERT: B 422 ARG cc_start: 0.8375 (mmm160) cc_final: 0.7903 (tpp-160) outliers start: 22 outliers final: 20 residues processed: 143 average time/residue: 0.2493 time to fit residues: 51.1440 Evaluate side-chains 137 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 199 HIS Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 431 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 100 optimal weight: 0.8980 chunk 129 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 143 optimal weight: 0.9980 chunk 112 optimal weight: 4.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 GLN A 224 ASN ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.117978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.094511 restraints weight = 16427.315| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 1.73 r_work: 0.2803 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 12303 Z= 0.136 Angle : 0.488 6.151 16713 Z= 0.256 Chirality : 0.039 0.119 1869 Planarity : 0.003 0.038 2085 Dihedral : 4.376 21.674 1593 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.17 % Allowed : 14.15 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.23), residues: 1443 helix: 1.08 (0.18), residues: 960 sheet: -1.19 (0.89), residues: 30 loop : -1.90 (0.25), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 180 HIS 0.003 0.001 HIS C 161 PHE 0.009 0.001 PHE A 79 TYR 0.015 0.001 TYR A 152 ARG 0.003 0.000 ARG A 146 Details of bonding type rmsd hydrogen bonds : bond 0.04541 ( 699) hydrogen bonds : angle 3.66854 ( 2025) SS BOND : bond 0.00100 ( 3) SS BOND : angle 0.86209 ( 6) covalent geometry : bond 0.00320 (12300) covalent geometry : angle 0.48736 (16707) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 122 time to evaluate : 1.578 Fit side-chains REVERT: A 422 ARG cc_start: 0.8350 (tpt-90) cc_final: 0.8055 (mmp80) REVERT: B 51 TYR cc_start: 0.9419 (t80) cc_final: 0.8837 (t80) REVERT: B 125 ARG cc_start: 0.8484 (ttm-80) cc_final: 0.7961 (ttm110) REVERT: B 146 ARG cc_start: 0.8532 (mtm180) cc_final: 0.8194 (mtm110) REVERT: B 159 GLU cc_start: 0.8585 (tm-30) cc_final: 0.8185 (tm-30) REVERT: B 422 ARG cc_start: 0.8347 (mmm160) cc_final: 0.7865 (tpp-160) REVERT: C 159 GLU cc_start: 0.8562 (tm-30) cc_final: 0.8302 (tm-30) REVERT: C 524 MET cc_start: 0.5746 (pmm) cc_final: 0.5326 (pmm) outliers start: 28 outliers final: 20 residues processed: 147 average time/residue: 0.2977 time to fit residues: 62.0756 Evaluate side-chains 139 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 1.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 520 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 66 optimal weight: 1.9990 chunk 136 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 22 optimal weight: 6.9990 chunk 87 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 121 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 124 optimal weight: 7.9990 chunk 92 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 ASN ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 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 = 0.3342 r_free = 0.3342 target = 0.124745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.101404 restraints weight = 16239.681| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 1.77 r_work: 0.2870 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 12303 Z= 0.100 Angle : 0.449 5.553 16713 Z= 0.236 Chirality : 0.037 0.118 1869 Planarity : 0.003 0.040 2085 Dihedral : 4.183 19.579 1593 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.86 % Allowed : 14.77 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.23), residues: 1443 helix: 1.41 (0.18), residues: 936 sheet: -1.24 (0.89), residues: 30 loop : -1.78 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 180 HIS 0.004 0.001 HIS C 161 PHE 0.009 0.001 PHE A 469 TYR 0.014 0.001 TYR A 152 ARG 0.002 0.000 ARG A 146 Details of bonding type rmsd hydrogen bonds : bond 0.04025 ( 699) hydrogen bonds : angle 3.52737 ( 2025) SS BOND : bond 0.00059 ( 3) SS BOND : angle 0.76225 ( 6) covalent geometry : bond 0.00212 (12300) covalent geometry : angle 0.44918 (16707) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 2.100 Fit side-chains REVERT: A 422 ARG cc_start: 0.8298 (tpt-90) cc_final: 0.7957 (mmp80) REVERT: B 51 TYR cc_start: 0.9375 (t80) cc_final: 0.9012 (t80) REVERT: B 125 ARG cc_start: 0.8486 (ttm-80) cc_final: 0.7976 (ttm110) REVERT: B 146 ARG cc_start: 0.8516 (mtm180) cc_final: 0.8182 (mtm110) REVERT: B 159 GLU cc_start: 0.8554 (tm-30) cc_final: 0.8145 (tm-30) REVERT: B 422 ARG cc_start: 0.8309 (mmm160) cc_final: 0.7814 (tpp-160) REVERT: C 159 GLU cc_start: 0.8544 (tm-30) cc_final: 0.8271 (tm-30) REVERT: C 422 ARG cc_start: 0.8694 (mmt90) cc_final: 0.8190 (mtp85) outliers start: 24 outliers final: 21 residues processed: 145 average time/residue: 0.2872 time to fit residues: 59.4491 Evaluate side-chains 136 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 323 GLU Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 520 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 89 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 75 optimal weight: 8.9990 chunk 119 optimal weight: 10.0000 chunk 99 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 chunk 80 optimal weight: 0.5980 chunk 126 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 137 optimal weight: 0.8980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 ASN ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 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 = 0.3275 r_free = 0.3275 target = 0.119413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.095914 restraints weight = 16508.145| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 1.74 r_work: 0.2847 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2700 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 12303 Z= 0.131 Angle : 0.471 5.572 16713 Z= 0.246 Chirality : 0.038 0.118 1869 Planarity : 0.003 0.041 2085 Dihedral : 4.217 19.175 1593 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.86 % Allowed : 15.31 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.23), residues: 1443 helix: 1.42 (0.18), residues: 936 sheet: -1.21 (0.90), residues: 30 loop : -1.67 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 180 HIS 0.003 0.001 HIS A 161 PHE 0.008 0.001 PHE A 469 TYR 0.014 0.001 TYR A 152 ARG 0.002 0.000 ARG A 146 Details of bonding type rmsd hydrogen bonds : bond 0.04353 ( 699) hydrogen bonds : angle 3.56374 ( 2025) SS BOND : bond 0.00106 ( 3) SS BOND : angle 0.69726 ( 6) covalent geometry : bond 0.00306 (12300) covalent geometry : angle 0.47106 (16707) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 2.092 Fit side-chains REVERT: A 422 ARG cc_start: 0.8328 (tpt-90) cc_final: 0.8067 (mmp80) REVERT: B 51 TYR cc_start: 0.9386 (t80) cc_final: 0.8926 (t80) REVERT: B 125 ARG cc_start: 0.8497 (ttm-80) cc_final: 0.7965 (ttm110) REVERT: B 146 ARG cc_start: 0.8552 (mtm180) cc_final: 0.8198 (mtm110) REVERT: B 159 GLU cc_start: 0.8605 (tm-30) cc_final: 0.8202 (tm-30) REVERT: B 422 ARG cc_start: 0.8317 (mmm160) cc_final: 0.7819 (tpp-160) REVERT: C 159 GLU cc_start: 0.8568 (tm-30) cc_final: 0.8306 (tm-30) REVERT: C 422 ARG cc_start: 0.8634 (mmt90) cc_final: 0.8151 (mtp85) REVERT: C 524 MET cc_start: 0.5525 (pmm) cc_final: 0.5079 (pmm) outliers start: 24 outliers final: 23 residues processed: 137 average time/residue: 0.2993 time to fit residues: 58.4374 Evaluate side-chains 139 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 323 GLU Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 520 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 27 optimal weight: 3.9990 chunk 114 optimal weight: 0.0170 chunk 22 optimal weight: 7.9990 chunk 87 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 131 optimal weight: 7.9990 chunk 138 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 117 optimal weight: 0.3980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 ASN ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 GLN ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.125302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.101899 restraints weight = 16188.340| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 1.78 r_work: 0.2891 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12303 Z= 0.093 Angle : 0.437 5.298 16713 Z= 0.229 Chirality : 0.037 0.118 1869 Planarity : 0.003 0.041 2085 Dihedral : 4.032 18.256 1593 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.78 % Allowed : 16.01 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.23), residues: 1443 helix: 1.58 (0.18), residues: 930 sheet: -1.30 (0.89), residues: 30 loop : -1.54 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 180 HIS 0.003 0.001 HIS C 161 PHE 0.009 0.001 PHE A 469 TYR 0.013 0.001 TYR A 152 ARG 0.002 0.000 ARG A 146 Details of bonding type rmsd hydrogen bonds : bond 0.03774 ( 699) hydrogen bonds : angle 3.45388 ( 2025) SS BOND : bond 0.00052 ( 3) SS BOND : angle 0.61137 ( 6) covalent geometry : bond 0.00191 (12300) covalent geometry : angle 0.43735 (16707) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 1.689 Fit side-chains REVERT: A 422 ARG cc_start: 0.8330 (tpt-90) cc_final: 0.8037 (mmp80) REVERT: B 125 ARG cc_start: 0.8483 (ttm-80) cc_final: 0.7981 (ttm110) REVERT: B 146 ARG cc_start: 0.8504 (mtm180) cc_final: 0.8153 (mtm110) REVERT: B 159 GLU cc_start: 0.8588 (tm-30) cc_final: 0.8171 (tm-30) REVERT: C 159 GLU cc_start: 0.8597 (tm-30) cc_final: 0.8324 (tm-30) REVERT: C 422 ARG cc_start: 0.8698 (mmt90) cc_final: 0.8192 (mtp85) REVERT: C 524 MET cc_start: 0.5660 (pmm) cc_final: 0.5205 (pmm) outliers start: 23 outliers final: 18 residues processed: 142 average time/residue: 0.3267 time to fit residues: 69.3919 Evaluate side-chains 131 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 1.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 323 GLU Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 520 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 64 optimal weight: 0.9990 chunk 122 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 123 optimal weight: 8.9990 chunk 42 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 116 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 chunk 114 optimal weight: 4.9990 chunk 131 optimal weight: 6.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 ASN ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.120279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.096749 restraints weight = 16485.362| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 1.73 r_work: 0.2873 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 12303 Z= 0.121 Angle : 0.460 6.716 16713 Z= 0.240 Chirality : 0.038 0.116 1869 Planarity : 0.003 0.042 2085 Dihedral : 4.103 17.933 1593 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.62 % Allowed : 15.93 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.23), residues: 1443 helix: 1.59 (0.18), residues: 930 sheet: -1.28 (0.89), residues: 30 loop : -1.52 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 180 HIS 0.003 0.001 HIS A 161 PHE 0.008 0.001 PHE A 465 TYR 0.014 0.001 TYR A 152 ARG 0.002 0.000 ARG A 146 Details of bonding type rmsd hydrogen bonds : bond 0.04140 ( 699) hydrogen bonds : angle 3.50300 ( 2025) SS BOND : bond 0.00118 ( 3) SS BOND : angle 0.57867 ( 6) covalent geometry : bond 0.00281 (12300) covalent geometry : angle 0.46012 (16707) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 1.908 Fit side-chains REVERT: A 422 ARG cc_start: 0.8336 (tpt-90) cc_final: 0.8080 (mmp80) REVERT: B 125 ARG cc_start: 0.8490 (ttm-80) cc_final: 0.7969 (ttm110) REVERT: B 146 ARG cc_start: 0.8533 (mtm180) cc_final: 0.8174 (mtm110) REVERT: B 159 GLU cc_start: 0.8605 (tm-30) cc_final: 0.8198 (tm-30) REVERT: B 422 ARG cc_start: 0.8311 (mmm160) cc_final: 0.7813 (tpp-160) REVERT: C 88 ASP cc_start: 0.7885 (p0) cc_final: 0.7584 (p0) REVERT: C 159 GLU cc_start: 0.8615 (tm-30) cc_final: 0.8347 (tm-30) REVERT: C 422 ARG cc_start: 0.8678 (mmt90) cc_final: 0.8183 (mtp85) outliers start: 21 outliers final: 18 residues processed: 138 average time/residue: 0.2885 time to fit residues: 57.9739 Evaluate side-chains 134 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 323 GLU Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 520 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 1 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 chunk 137 optimal weight: 0.0040 chunk 76 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 126 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 69 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 overall best weight: 1.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 HIS A 184 GLN A 224 ASN ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 GLN ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.120295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.096815 restraints weight = 16391.328| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 1.72 r_work: 0.2883 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12303 Z= 0.116 Angle : 0.461 6.053 16713 Z= 0.241 Chirality : 0.038 0.120 1869 Planarity : 0.003 0.042 2085 Dihedral : 4.102 18.238 1593 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.70 % Allowed : 16.16 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.80 (0.23), residues: 1443 helix: 1.59 (0.18), residues: 930 sheet: -1.25 (0.89), residues: 30 loop : -1.50 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 180 HIS 0.003 0.001 HIS C 161 PHE 0.008 0.001 PHE A 465 TYR 0.015 0.001 TYR B 51 ARG 0.002 0.000 ARG A 146 Details of bonding type rmsd hydrogen bonds : bond 0.04118 ( 699) hydrogen bonds : angle 3.50264 ( 2025) SS BOND : bond 0.00099 ( 3) SS BOND : angle 0.59022 ( 6) covalent geometry : bond 0.00265 (12300) covalent geometry : angle 0.46129 (16707) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 1.367 Fit side-chains REVERT: A 422 ARG cc_start: 0.8325 (tpt-90) cc_final: 0.8067 (mmp80) REVERT: B 125 ARG cc_start: 0.8491 (ttm-80) cc_final: 0.7972 (ttm110) REVERT: B 146 ARG cc_start: 0.8539 (mtm180) cc_final: 0.8182 (mtm110) REVERT: B 159 GLU cc_start: 0.8610 (tm-30) cc_final: 0.8225 (tm-30) REVERT: C 159 GLU cc_start: 0.8620 (tm-30) cc_final: 0.8355 (tm-30) REVERT: C 422 ARG cc_start: 0.8674 (mmt90) cc_final: 0.8184 (mtp85) outliers start: 22 outliers final: 18 residues processed: 132 average time/residue: 0.2551 time to fit residues: 48.1127 Evaluate side-chains 132 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 323 GLU Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 520 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 85 optimal weight: 0.5980 chunk 119 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 113 optimal weight: 0.8980 chunk 72 optimal weight: 6.9990 chunk 111 optimal weight: 10.0000 chunk 138 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 105 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 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 = 0.3300 r_free = 0.3300 target = 0.121382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.098163 restraints weight = 16300.598| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 1.71 r_work: 0.2903 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12303 Z= 0.104 Angle : 0.454 5.914 16713 Z= 0.237 Chirality : 0.037 0.119 1869 Planarity : 0.003 0.042 2085 Dihedral : 4.075 17.875 1593 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.47 % Allowed : 16.40 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.23), residues: 1443 helix: 1.63 (0.18), residues: 930 sheet: -1.26 (0.89), residues: 30 loop : -1.48 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 180 HIS 0.003 0.001 HIS C 161 PHE 0.008 0.001 PHE A 469 TYR 0.014 0.001 TYR B 51 ARG 0.002 0.000 ARG A 146 Details of bonding type rmsd hydrogen bonds : bond 0.04002 ( 699) hydrogen bonds : angle 3.47329 ( 2025) SS BOND : bond 0.00078 ( 3) SS BOND : angle 0.58589 ( 6) covalent geometry : bond 0.00231 (12300) covalent geometry : angle 0.45375 (16707) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 1.319 Fit side-chains REVERT: A 422 ARG cc_start: 0.8266 (tpt-90) cc_final: 0.7980 (mmp80) REVERT: B 125 ARG cc_start: 0.8478 (ttm-80) cc_final: 0.7969 (ttm110) REVERT: B 146 ARG cc_start: 0.8525 (mtm180) cc_final: 0.8173 (mtm110) REVERT: B 159 GLU cc_start: 0.8609 (tm-30) cc_final: 0.8221 (tm-30) REVERT: C 88 ASP cc_start: 0.7920 (p0) cc_final: 0.7647 (p0) REVERT: C 159 GLU cc_start: 0.8610 (tm-30) cc_final: 0.8344 (tm-30) REVERT: C 422 ARG cc_start: 0.8662 (mmt90) cc_final: 0.8173 (mtp85) outliers start: 19 outliers final: 18 residues processed: 134 average time/residue: 0.2702 time to fit residues: 52.2609 Evaluate side-chains 130 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 1.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 323 GLU Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 520 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 117 optimal weight: 0.9980 chunk 96 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 141 optimal weight: 7.9990 chunk 38 optimal weight: 0.0050 chunk 140 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 overall best weight: 1.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 GLN ** C 161 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 = 0.3304 r_free = 0.3304 target = 0.121695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.097910 restraints weight = 16252.323| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 1.79 r_work: 0.2862 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12303 Z= 0.126 Angle : 0.470 5.977 16713 Z= 0.246 Chirality : 0.038 0.117 1869 Planarity : 0.003 0.042 2085 Dihedral : 4.146 18.523 1593 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.47 % Allowed : 16.71 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.23), residues: 1443 helix: 1.58 (0.18), residues: 936 sheet: -1.24 (0.90), residues: 30 loop : -1.47 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 180 HIS 0.003 0.001 HIS C 161 PHE 0.008 0.001 PHE A 465 TYR 0.015 0.001 TYR B 51 ARG 0.001 0.000 ARG B 527 Details of bonding type rmsd hydrogen bonds : bond 0.04261 ( 699) hydrogen bonds : angle 3.55372 ( 2025) SS BOND : bond 0.00118 ( 3) SS BOND : angle 0.59074 ( 6) covalent geometry : bond 0.00293 (12300) covalent geometry : angle 0.47016 (16707) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6382.91 seconds wall clock time: 118 minutes 41.22 seconds (7121.22 seconds total)