Starting phenix.real_space_refine on Sat Aug 23 16:55:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hob_34924/08_2025/8hob_34924_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hob_34924/08_2025/8hob_34924.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hob_34924/08_2025/8hob_34924.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hob_34924/08_2025/8hob_34924.map" model { file = "/net/cci-nas-00/data/ceres_data/8hob_34924/08_2025/8hob_34924_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hob_34924/08_2025/8hob_34924_neut.cif" } resolution = 2.19 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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 36 5.16 5 C 8402 2.51 5 N 2190 2.21 5 O 2821 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13449 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 811, 6558 Classifications: {'peptide': 811} Link IDs: {'PCIS': 3, 'PTRANS': 26, 'TRANS': 781} Chain: "B" Number of atoms: 6558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 811, 6558 Classifications: {'peptide': 811} Link IDs: {'PCIS': 3, 'PTRANS': 26, 'TRANS': 781} Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Classifications: {'water': 175} Link IDs: {None: 174} Chain: "B" Number of atoms: 158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 158 Classifications: {'water': 158} Link IDs: {None: 157} Time building chain proxies: 2.66, per 1000 atoms: 0.20 Number of scatterers: 13449 At special positions: 0 Unit cell: (145.25, 95.45, 97.11, 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 36 16.00 O 2821 8.00 N 2190 7.00 C 8402 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.12 Conformation dependent library (CDL) restraints added in 713.0 milliseconds Enol-peptide restraints added in 1.2 microseconds 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2976 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 25 sheets defined 33.9% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 157 through 164 Processing helix chain 'A' and resid 164 through 169 Processing helix chain 'A' and resid 210 through 214 Processing helix chain 'A' and resid 223 through 229 Processing helix chain 'A' and resid 269 through 272 Processing helix chain 'A' and resid 282 through 292 removed outlier: 3.811A pdb=" N PHE A 292 " --> pdb=" O MET A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 313 Processing helix chain 'A' and resid 322 through 331 Processing helix chain 'A' and resid 331 through 344 Processing helix chain 'A' and resid 360 through 371 removed outlier: 3.710A pdb=" N LEU A 367 " --> pdb=" O SER A 363 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU A 368 " --> pdb=" O ASN A 364 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLY A 369 " --> pdb=" O GLN A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 388 removed outlier: 3.697A pdb=" N THR A 388 " --> pdb=" O ASP A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 433 removed outlier: 3.978A pdb=" N TRP A 420 " --> pdb=" O ASP A 416 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU A 421 " --> pdb=" O ASP A 417 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE A 422 " --> pdb=" O PRO A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 439 removed outlier: 3.788A pdb=" N ILE A 437 " --> pdb=" O ASP A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 467 removed outlier: 3.989A pdb=" N VAL A 465 " --> pdb=" O SER A 461 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL A 466 " --> pdb=" O PHE A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.951A pdb=" N LYS A 524 " --> pdb=" O VAL A 520 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ASP A 525 " --> pdb=" O PHE A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 557 Processing helix chain 'A' and resid 586 through 595 removed outlier: 3.719A pdb=" N GLY A 590 " --> pdb=" O ILE A 586 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N PHE A 591 " --> pdb=" O GLU A 587 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER A 592 " --> pdb=" O SER A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 615 Processing helix chain 'A' and resid 635 through 641 removed outlier: 4.499A pdb=" N ILE A 638 " --> pdb=" O TYR A 635 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER A 639 " --> pdb=" O GLY A 636 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TYR A 641 " --> pdb=" O ILE A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 666 removed outlier: 4.067A pdb=" N TRP A 658 " --> pdb=" O HIS A 654 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE A 659 " --> pdb=" O ASN A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 680 removed outlier: 3.768A pdb=" N ILE A 679 " --> pdb=" O TYR A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 685 Processing helix chain 'A' and resid 687 through 692 Processing helix chain 'A' and resid 720 through 731 removed outlier: 3.557A pdb=" N TRP A 724 " --> pdb=" O GLY A 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 164 Processing helix chain 'B' and resid 164 through 169 Processing helix chain 'B' and resid 210 through 214 Processing helix chain 'B' and resid 223 through 229 Processing helix chain 'B' and resid 282 through 292 removed outlier: 3.857A pdb=" N PHE B 292 " --> pdb=" O MET B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 313 Processing helix chain 'B' and resid 322 through 331 Processing helix chain 'B' and resid 331 through 344 Processing helix chain 'B' and resid 360 through 371 removed outlier: 3.710A pdb=" N LEU B 368 " --> pdb=" O ASN B 364 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY B 369 " --> pdb=" O GLN B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 388 removed outlier: 3.693A pdb=" N THR B 388 " --> pdb=" O ASP B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 433 removed outlier: 4.007A pdb=" N TRP B 420 " --> pdb=" O ASP B 416 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU B 421 " --> pdb=" O ASP B 417 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE B 422 " --> pdb=" O PRO B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 439 removed outlier: 3.744A pdb=" N ILE B 437 " --> pdb=" O ASP B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 467 removed outlier: 3.991A pdb=" N VAL B 465 " --> pdb=" O SER B 461 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL B 466 " --> pdb=" O PHE B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 533 removed outlier: 4.012A pdb=" N LYS B 524 " --> pdb=" O VAL B 520 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ASP B 525 " --> pdb=" O PHE B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 557 Processing helix chain 'B' and resid 586 through 595 removed outlier: 3.714A pdb=" N GLY B 590 " --> pdb=" O ILE B 586 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N PHE B 591 " --> pdb=" O GLU B 587 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER B 592 " --> pdb=" O SER B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 615 Processing helix chain 'B' and resid 635 through 641 removed outlier: 4.514A pdb=" N ILE B 638 " --> pdb=" O TYR B 635 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N SER B 639 " --> pdb=" O GLY B 636 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TYR B 641 " --> pdb=" O ILE B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 666 removed outlier: 4.070A pdb=" N TRP B 658 " --> pdb=" O HIS B 654 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE B 659 " --> pdb=" O ASN B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 680 removed outlier: 3.763A pdb=" N ILE B 679 " --> pdb=" O TYR B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 685 Processing helix chain 'B' and resid 687 through 692 Processing helix chain 'B' and resid 720 through 731 removed outlier: 3.556A pdb=" N TRP B 724 " --> pdb=" O GLY B 720 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 8 removed outlier: 3.652A pdb=" N SER A 95 " --> pdb=" O LYS A 110 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 29 Processing sheet with id=AA3, first strand: chain 'A' and resid 55 through 57 removed outlier: 5.553A pdb=" N ILE A 56 " --> pdb=" O SER A 154 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 55 through 57 removed outlier: 5.553A pdb=" N ILE A 56 " --> pdb=" O SER A 154 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N SER A 208 " --> pdb=" O ILE A 242 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N SER A 244 " --> pdb=" O PHE A 206 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N PHE A 206 " --> pdb=" O SER A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 274 through 276 removed outlier: 6.832A pdb=" N VAL A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 316 through 319 Processing sheet with id=AA7, first strand: chain 'A' and resid 358 through 359 Processing sheet with id=AA8, first strand: chain 'A' and resid 441 through 444 removed outlier: 3.970A pdb=" N PHE A 444 " --> pdb=" O LYS A 450 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N LYS A 450 " --> pdb=" O PHE A 444 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 511 through 512 Processing sheet with id=AB1, first strand: chain 'A' and resid 584 through 585 Processing sheet with id=AB2, first strand: chain 'A' and resid 616 through 617 Processing sheet with id=AB3, first strand: chain 'A' and resid 699 through 702 removed outlier: 6.632A pdb=" N ALA A 699 " --> pdb=" O SER A 716 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N SER A 716 " --> pdb=" O ALA A 699 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 736 through 739 removed outlier: 3.879A pdb=" N LEU A 743 " --> pdb=" O LEU A 796 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 5 through 8 removed outlier: 3.649A pdb=" N SER B 95 " --> pdb=" O LYS B 110 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 26 through 29 Processing sheet with id=AB7, first strand: chain 'B' and resid 80 through 82 removed outlier: 3.743A pdb=" N HIS B 245 " --> pdb=" O SER B 149 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N SER B 208 " --> pdb=" O ILE B 242 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N SER B 244 " --> pdb=" O PHE B 206 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N PHE B 206 " --> pdb=" O SER B 244 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 274 through 276 removed outlier: 6.848A pdb=" N VAL B 279 " --> pdb=" O GLU B 275 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 316 through 319 Processing sheet with id=AC1, first strand: chain 'B' and resid 358 through 359 Processing sheet with id=AC2, first strand: chain 'B' and resid 441 through 444 removed outlier: 3.949A pdb=" N PHE B 444 " --> pdb=" O LYS B 450 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N LYS B 450 " --> pdb=" O PHE B 444 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 511 through 512 Processing sheet with id=AC4, first strand: chain 'B' and resid 584 through 585 Processing sheet with id=AC5, first strand: chain 'B' and resid 616 through 617 Processing sheet with id=AC6, first strand: chain 'B' and resid 699 through 702 removed outlier: 6.631A pdb=" N ALA B 699 " --> pdb=" O SER B 716 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N SER B 716 " --> pdb=" O ALA B 699 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 736 through 739 removed outlier: 3.891A pdb=" N LEU B 743 " --> pdb=" O LEU B 796 " (cutoff:3.500A) 578 hydrogen bonds defined for protein. 1623 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: 2.96 Time building geometry restraints manager: 1.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.79 - 0.99: 4 0.99 - 1.20: 4 1.20 - 1.40: 5863 1.40 - 1.61: 7523 1.61 - 1.81: 68 Bond restraints: 13462 Sorted by residual: bond pdb=" C GLN B 166 " pdb=" O GLN B 166 " ideal model delta sigma weight residual 1.236 0.791 0.445 1.18e-02 7.18e+03 1.42e+03 bond pdb=" C ASN B 168 " pdb=" O ASN B 168 " ideal model delta sigma weight residual 1.236 0.822 0.414 1.28e-02 6.10e+03 1.04e+03 bond pdb=" C ARG B 167 " pdb=" O ARG B 167 " ideal model delta sigma weight residual 1.235 0.933 0.301 1.03e-02 9.43e+03 8.56e+02 bond pdb=" C PHE B 165 " pdb=" O PHE B 165 " ideal model delta sigma weight residual 1.236 0.904 0.332 1.26e-02 6.30e+03 6.96e+02 bond pdb=" CA GLN B 166 " pdb=" C GLN B 166 " ideal model delta sigma weight residual 1.523 1.290 0.233 1.35e-02 5.49e+03 2.98e+02 ... (remaining 13457 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.42: 18181 6.42 - 12.85: 14 12.85 - 19.27: 7 19.27 - 25.69: 2 25.69 - 32.12: 2 Bond angle restraints: 18206 Sorted by residual: angle pdb=" N GLN B 166 " pdb=" CA GLN B 166 " pdb=" CB GLN B 166 " ideal model delta sigma weight residual 110.06 80.76 29.30 1.50e+00 4.44e-01 3.82e+02 angle pdb=" C GLN B 166 " pdb=" CA GLN B 166 " pdb=" CB GLN B 166 " ideal model delta sigma weight residual 110.68 142.80 -32.12 1.70e+00 3.46e-01 3.57e+02 angle pdb=" CA ASN B 168 " pdb=" CB ASN B 168 " pdb=" CG ASN B 168 " ideal model delta sigma weight residual 112.60 129.82 -17.22 1.00e+00 1.00e+00 2.97e+02 angle pdb=" CA PHE B 165 " pdb=" CB PHE B 165 " pdb=" CG PHE B 165 " ideal model delta sigma weight residual 113.80 128.11 -14.31 1.00e+00 1.00e+00 2.05e+02 angle pdb=" C ASN B 164 " pdb=" N PHE B 165 " pdb=" CA PHE B 165 " ideal model delta sigma weight residual 120.31 142.04 -21.73 1.52e+00 4.33e-01 2.04e+02 ... (remaining 18201 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 6862 17.93 - 35.86: 730 35.86 - 53.78: 229 53.78 - 71.71: 50 71.71 - 89.64: 21 Dihedral angle restraints: 7892 sinusoidal: 3192 harmonic: 4700 Sorted by residual: dihedral pdb=" C GLN B 166 " pdb=" N GLN B 166 " pdb=" CA GLN B 166 " pdb=" CB GLN B 166 " ideal model delta harmonic sigma weight residual -122.60 -148.42 25.82 0 2.50e+00 1.60e-01 1.07e+02 dihedral pdb=" C ARG B 167 " pdb=" N ARG B 167 " pdb=" CA ARG B 167 " pdb=" CB ARG B 167 " ideal model delta harmonic sigma weight residual -122.60 -144.26 21.66 0 2.50e+00 1.60e-01 7.51e+01 dihedral pdb=" C PHE B 165 " pdb=" N PHE B 165 " pdb=" CA PHE B 165 " pdb=" CB PHE B 165 " ideal model delta harmonic sigma weight residual -122.60 -143.69 21.09 0 2.50e+00 1.60e-01 7.12e+01 ... (remaining 7889 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.290: 1854 0.290 - 0.580: 0 0.580 - 0.870: 1 0.870 - 1.160: 2 1.160 - 1.450: 1 Chirality restraints: 1858 Sorted by residual: chirality pdb=" CA GLN B 166 " pdb=" N GLN B 166 " pdb=" C GLN B 166 " pdb=" CB GLN B 166 " both_signs ideal model delta sigma weight residual False 2.51 1.06 1.45 2.00e-01 2.50e+01 5.26e+01 chirality pdb=" CA PHE B 165 " pdb=" N PHE B 165 " pdb=" C PHE B 165 " pdb=" CB PHE B 165 " both_signs ideal model delta sigma weight residual False 2.51 1.54 0.97 2.00e-01 2.50e+01 2.36e+01 chirality pdb=" CA ARG B 167 " pdb=" N ARG B 167 " pdb=" C ARG B 167 " pdb=" CB ARG B 167 " both_signs ideal model delta sigma weight residual False 2.51 1.55 0.96 2.00e-01 2.50e+01 2.32e+01 ... (remaining 1855 not shown) Planarity restraints: 2372 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 168 " 0.030 2.00e-02 2.50e+03 7.53e-02 5.67e+01 pdb=" C ASN B 168 " -0.129 2.00e-02 2.50e+03 pdb=" O ASN B 168 " 0.061 2.00e-02 2.50e+03 pdb=" N PHE B 169 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 165 " 0.019 2.00e-02 2.50e+03 4.30e-02 1.84e+01 pdb=" C PHE B 165 " -0.074 2.00e-02 2.50e+03 pdb=" O PHE B 165 " 0.030 2.00e-02 2.50e+03 pdb=" N GLN B 166 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 165 " 0.004 2.00e-02 2.50e+03 2.88e-02 1.45e+01 pdb=" CG PHE B 165 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 PHE B 165 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 PHE B 165 " -0.036 2.00e-02 2.50e+03 pdb=" CE1 PHE B 165 " 0.027 2.00e-02 2.50e+03 pdb=" CE2 PHE B 165 " 0.040 2.00e-02 2.50e+03 pdb=" CZ PHE B 165 " -0.033 2.00e-02 2.50e+03 ... (remaining 2369 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2296 2.76 - 3.30: 12140 3.30 - 3.83: 25906 3.83 - 4.37: 32785 4.37 - 4.90: 50930 Nonbonded interactions: 124057 Sorted by model distance: nonbonded pdb=" OD2 ASP A 706 " pdb=" O HOH A 901 " model vdw 2.230 3.040 nonbonded pdb=" OG1 THR B 31 " pdb=" OE2 GLU B 32 " model vdw 2.247 3.040 nonbonded pdb=" OD1 ASP A 209 " pdb=" O HOH A 902 " model vdw 2.262 3.040 nonbonded pdb=" OD1 ASP B 209 " pdb=" O HOH B 901 " model vdw 2.265 3.040 nonbonded pdb=" OD1 ASP A 160 " pdb=" O HOH A 903 " model vdw 2.268 3.040 ... (remaining 124052 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' 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: 7.160 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: 0.280 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.650 Find NCS groups from input model: 0.160 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:6.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 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 : 0.008 0.445 13462 Z= 0.649 Angle : 0.753 32.118 18206 Z= 0.482 Chirality : 0.066 1.450 1858 Planarity : 0.005 0.083 2372 Dihedral : 17.238 89.641 4916 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.23 % Allowed : 17.05 % Favored : 81.72 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.21), residues: 1618 helix: 1.14 (0.24), residues: 482 sheet: 1.27 (0.30), residues: 282 loop : -0.19 (0.22), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.054 0.001 ARG B 167 TYR 0.014 0.001 TYR A 526 PHE 0.040 0.002 PHE B 165 TRP 0.013 0.001 TRP B 332 HIS 0.003 0.001 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00845 (13462) covalent geometry : angle 0.75311 (18206) hydrogen bonds : bond 0.11933 ( 577) hydrogen bonds : angle 6.20292 ( 1623) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 0.459 Fit side-chains REVERT: A 258 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7991 (mt-10) REVERT: B 167 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.7336 (ttt180) outliers start: 17 outliers final: 14 residues processed: 147 average time/residue: 0.7482 time to fit residues: 117.4315 Evaluate side-chains 143 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 790 GLU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 166 GLN Chi-restraints excluded: chain B residue 167 ARG Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 363 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 389 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.099092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.086854 restraints weight = 14368.989| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 1.27 r_work: 0.2908 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.0444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13462 Z= 0.156 Angle : 0.543 5.971 18206 Z= 0.305 Chirality : 0.047 0.160 1858 Planarity : 0.004 0.038 2372 Dihedral : 7.265 78.271 1827 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.66 % Allowed : 16.62 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.21), residues: 1618 helix: 1.20 (0.23), residues: 484 sheet: 1.26 (0.30), residues: 282 loop : -0.22 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 356 TYR 0.015 0.002 TYR A 526 PHE 0.021 0.002 PHE B 370 TRP 0.016 0.001 TRP B 332 HIS 0.005 0.001 HIS B 545 Details of bonding type rmsd covalent geometry : bond 0.00351 (13462) covalent geometry : angle 0.54284 (18206) hydrogen bonds : bond 0.04847 ( 577) hydrogen bonds : angle 5.72779 ( 1623) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 0.452 Fit side-chains REVERT: A 160 ASP cc_start: 0.8638 (t70) cc_final: 0.8428 (t70) REVERT: A 258 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8305 (mt-10) REVERT: A 538 GLU cc_start: 0.7983 (mp0) cc_final: 0.7675 (mp0) REVERT: B 138 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8174 (mt-10) REVERT: B 258 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8392 (mt-10) outliers start: 23 outliers final: 12 residues processed: 147 average time/residue: 0.8141 time to fit residues: 127.6806 Evaluate side-chains 141 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 790 GLU Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 792 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 123 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 77 optimal weight: 0.2980 chunk 143 optimal weight: 1.9990 chunk 90 optimal weight: 0.0570 chunk 139 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.101233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.089097 restraints weight = 14480.655| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.27 r_work: 0.2945 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.0514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13462 Z= 0.107 Angle : 0.490 5.179 18206 Z= 0.275 Chirality : 0.044 0.140 1858 Planarity : 0.004 0.038 2372 Dihedral : 6.502 72.328 1812 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.59 % Allowed : 16.62 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.21), residues: 1618 helix: 1.40 (0.24), residues: 478 sheet: 1.17 (0.30), residues: 284 loop : -0.15 (0.22), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 356 TYR 0.012 0.001 TYR B 14 PHE 0.021 0.001 PHE B 370 TRP 0.015 0.001 TRP B 332 HIS 0.003 0.001 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.00224 (13462) covalent geometry : angle 0.48977 (18206) hydrogen bonds : bond 0.04049 ( 577) hydrogen bonds : angle 5.53467 ( 1623) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 0.567 Fit side-chains REVERT: A 91 ARG cc_start: 0.9044 (OUTLIER) cc_final: 0.8231 (mtt180) REVERT: A 160 ASP cc_start: 0.8582 (t70) cc_final: 0.8378 (t70) REVERT: A 538 GLU cc_start: 0.7899 (mp0) cc_final: 0.7556 (mp0) REVERT: B 258 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8330 (mt-10) REVERT: B 380 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7578 (tt0) REVERT: B 538 GLU cc_start: 0.7921 (mp0) cc_final: 0.7711 (mp0) outliers start: 22 outliers final: 12 residues processed: 143 average time/residue: 0.7607 time to fit residues: 116.3683 Evaluate side-chains 142 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 790 GLU Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 792 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 128 optimal weight: 0.6980 chunk 130 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 147 optimal weight: 0.8980 chunk 148 optimal weight: 0.7980 chunk 158 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 108 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.099560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.087338 restraints weight = 14343.496| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 1.27 r_work: 0.2918 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.0554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13462 Z= 0.145 Angle : 0.526 5.337 18206 Z= 0.295 Chirality : 0.046 0.143 1858 Planarity : 0.004 0.039 2372 Dihedral : 6.198 57.272 1808 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.10 % Allowed : 15.97 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.21), residues: 1618 helix: 1.33 (0.24), residues: 478 sheet: 1.37 (0.30), residues: 272 loop : -0.22 (0.22), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 356 TYR 0.014 0.001 TYR A 14 PHE 0.021 0.002 PHE B 370 TRP 0.016 0.001 TRP B 332 HIS 0.004 0.001 HIS B 545 Details of bonding type rmsd covalent geometry : bond 0.00326 (13462) covalent geometry : angle 0.52598 (18206) hydrogen bonds : bond 0.04526 ( 577) hydrogen bonds : angle 5.59386 ( 1623) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 129 time to evaluate : 0.451 Fit side-chains REVERT: A 91 ARG cc_start: 0.9061 (OUTLIER) cc_final: 0.8279 (mtt180) REVERT: A 160 ASP cc_start: 0.8596 (t70) cc_final: 0.8349 (t70) REVERT: A 538 GLU cc_start: 0.7925 (mp0) cc_final: 0.7681 (mp0) REVERT: B 258 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.8381 (mt-10) REVERT: B 380 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7607 (tt0) REVERT: B 538 GLU cc_start: 0.7939 (mp0) cc_final: 0.7715 (mp0) outliers start: 29 outliers final: 14 residues processed: 148 average time/residue: 0.8143 time to fit residues: 128.5278 Evaluate side-chains 146 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 358 MET Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 737 LYS Chi-restraints excluded: chain A residue 790 GLU Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 792 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 158 optimal weight: 0.0270 chunk 116 optimal weight: 0.6980 chunk 157 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 90 optimal weight: 0.7980 chunk 103 optimal weight: 0.5980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.101298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.089165 restraints weight = 14413.702| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 1.27 r_work: 0.2948 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.0576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13462 Z= 0.109 Angle : 0.488 4.975 18206 Z= 0.274 Chirality : 0.044 0.141 1858 Planarity : 0.004 0.039 2372 Dihedral : 6.035 56.673 1808 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.52 % Allowed : 16.69 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.81 (0.21), residues: 1618 helix: 1.42 (0.24), residues: 478 sheet: 1.37 (0.30), residues: 272 loop : -0.20 (0.22), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 356 TYR 0.012 0.001 TYR A 14 PHE 0.020 0.001 PHE B 370 TRP 0.016 0.001 TRP B 332 HIS 0.003 0.001 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.00230 (13462) covalent geometry : angle 0.48822 (18206) hydrogen bonds : bond 0.03974 ( 577) hydrogen bonds : angle 5.45800 ( 1623) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 0.559 Fit side-chains REVERT: A 91 ARG cc_start: 0.9044 (OUTLIER) cc_final: 0.8258 (mtt180) REVERT: A 160 ASP cc_start: 0.8511 (t70) cc_final: 0.8274 (t70) REVERT: A 258 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8330 (mt-10) REVERT: A 538 GLU cc_start: 0.7910 (mp0) cc_final: 0.7589 (mp0) REVERT: B 138 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8119 (mt-10) REVERT: B 258 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8299 (mt-10) REVERT: B 380 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7574 (tt0) outliers start: 21 outliers final: 14 residues processed: 145 average time/residue: 0.7781 time to fit residues: 120.6990 Evaluate side-chains 145 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 790 GLU Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 792 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 90 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 50 optimal weight: 6.9990 chunk 105 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 89 optimal weight: 0.6980 chunk 117 optimal weight: 0.7980 chunk 132 optimal weight: 6.9990 chunk 126 optimal weight: 5.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN A 291 GLN B 140 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.097308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.085030 restraints weight = 14389.724| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 1.27 r_work: 0.2878 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.0689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 13462 Z= 0.221 Angle : 0.602 5.838 18206 Z= 0.337 Chirality : 0.050 0.146 1858 Planarity : 0.005 0.044 2372 Dihedral : 6.406 57.016 1807 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.17 % Allowed : 15.68 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.21), residues: 1618 helix: 1.12 (0.23), residues: 480 sheet: 1.30 (0.29), residues: 282 loop : -0.29 (0.22), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 356 TYR 0.019 0.002 TYR A 526 PHE 0.021 0.002 PHE A 370 TRP 0.018 0.002 TRP B 332 HIS 0.006 0.001 HIS B 545 Details of bonding type rmsd covalent geometry : bond 0.00515 (13462) covalent geometry : angle 0.60217 (18206) hydrogen bonds : bond 0.05420 ( 577) hydrogen bonds : angle 5.76136 ( 1623) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 127 time to evaluate : 0.377 Fit side-chains REVERT: A 91 ARG cc_start: 0.9093 (OUTLIER) cc_final: 0.8321 (mtt180) REVERT: A 160 ASP cc_start: 0.8661 (t70) cc_final: 0.8390 (t70) REVERT: A 258 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8358 (mt-10) REVERT: A 380 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7682 (tt0) REVERT: A 538 GLU cc_start: 0.7926 (mp0) cc_final: 0.7632 (mp0) REVERT: B 138 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8220 (mt-10) REVERT: B 258 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8381 (mt-10) REVERT: B 380 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7673 (tt0) REVERT: B 600 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7983 (mp0) outliers start: 30 outliers final: 16 residues processed: 145 average time/residue: 0.7788 time to fit residues: 120.6632 Evaluate side-chains 145 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 380 GLU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 737 LYS Chi-restraints excluded: chain A residue 790 GLU Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 600 GLU Chi-restraints excluded: chain B residue 792 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 140 optimal weight: 5.9990 chunk 143 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 126 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 137 optimal weight: 0.9990 chunk 159 optimal weight: 0.8980 chunk 131 optimal weight: 0.6980 chunk 123 optimal weight: 1.9990 chunk 129 optimal weight: 0.5980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.099013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.086823 restraints weight = 14361.486| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 1.26 r_work: 0.2909 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.0645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13462 Z= 0.145 Angle : 0.537 5.522 18206 Z= 0.301 Chirality : 0.046 0.143 1858 Planarity : 0.004 0.044 2372 Dihedral : 6.280 57.904 1807 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.59 % Allowed : 16.47 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.21), residues: 1618 helix: 1.23 (0.24), residues: 476 sheet: 1.36 (0.30), residues: 272 loop : -0.26 (0.22), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 356 TYR 0.014 0.001 TYR A 14 PHE 0.020 0.002 PHE B 370 TRP 0.017 0.001 TRP B 332 HIS 0.003 0.001 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.00324 (13462) covalent geometry : angle 0.53692 (18206) hydrogen bonds : bond 0.04632 ( 577) hydrogen bonds : angle 5.63626 ( 1623) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 0.508 Fit side-chains REVERT: A 91 ARG cc_start: 0.9084 (OUTLIER) cc_final: 0.8301 (mtt180) REVERT: A 160 ASP cc_start: 0.8603 (t70) cc_final: 0.8343 (t70) REVERT: A 258 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8328 (mt-10) REVERT: A 270 ASP cc_start: 0.8659 (m-30) cc_final: 0.8454 (m-30) REVERT: A 380 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7654 (tt0) REVERT: A 538 GLU cc_start: 0.7922 (mp0) cc_final: 0.7666 (mp0) REVERT: B 138 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8182 (mt-10) REVERT: B 258 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8361 (mt-10) REVERT: B 380 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7646 (tt0) outliers start: 22 outliers final: 16 residues processed: 145 average time/residue: 0.7837 time to fit residues: 121.3395 Evaluate side-chains 150 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 380 GLU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 524 LYS Chi-restraints excluded: chain A residue 737 LYS Chi-restraints excluded: chain A residue 790 GLU Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 792 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 68 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 chunk 137 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 151 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.097284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.085005 restraints weight = 14357.674| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 1.27 r_work: 0.2879 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.0731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13462 Z= 0.213 Angle : 0.600 6.508 18206 Z= 0.336 Chirality : 0.049 0.147 1858 Planarity : 0.005 0.045 2372 Dihedral : 6.461 57.778 1807 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.95 % Allowed : 15.82 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.21), residues: 1618 helix: 1.07 (0.23), residues: 480 sheet: 1.14 (0.29), residues: 294 loop : -0.27 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 356 TYR 0.018 0.002 TYR A 526 PHE 0.021 0.002 PHE B 370 TRP 0.018 0.002 TRP B 332 HIS 0.005 0.001 HIS B 545 Details of bonding type rmsd covalent geometry : bond 0.00495 (13462) covalent geometry : angle 0.60008 (18206) hydrogen bonds : bond 0.05364 ( 577) hydrogen bonds : angle 5.77544 ( 1623) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 128 time to evaluate : 0.534 Fit side-chains REVERT: A 91 ARG cc_start: 0.9103 (OUTLIER) cc_final: 0.8328 (mtt180) REVERT: A 160 ASP cc_start: 0.8666 (t70) cc_final: 0.8388 (t70) REVERT: A 258 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8364 (mt-10) REVERT: A 270 ASP cc_start: 0.8654 (m-30) cc_final: 0.8423 (m-30) REVERT: A 380 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7690 (tt0) REVERT: A 538 GLU cc_start: 0.7930 (mp0) cc_final: 0.7638 (mp0) REVERT: A 540 ARG cc_start: 0.7777 (mtm-85) cc_final: 0.7492 (mtm-85) REVERT: B 91 ARG cc_start: 0.9084 (OUTLIER) cc_final: 0.8160 (mtt180) REVERT: B 138 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8237 (mt-10) REVERT: B 258 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.8381 (mt-10) REVERT: B 380 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7669 (tt0) outliers start: 27 outliers final: 17 residues processed: 147 average time/residue: 0.7621 time to fit residues: 119.8782 Evaluate side-chains 149 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 380 GLU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 524 LYS Chi-restraints excluded: chain A residue 737 LYS Chi-restraints excluded: chain A residue 790 GLU Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 792 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 159 optimal weight: 0.1980 chunk 136 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 84 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 138 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 113 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.099126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.086886 restraints weight = 14406.112| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 1.27 r_work: 0.2910 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.0664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13462 Z= 0.143 Angle : 0.538 5.571 18206 Z= 0.301 Chirality : 0.046 0.143 1858 Planarity : 0.004 0.044 2372 Dihedral : 6.289 58.319 1807 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.81 % Allowed : 15.97 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.21), residues: 1618 helix: 1.23 (0.24), residues: 476 sheet: 1.33 (0.30), residues: 272 loop : -0.25 (0.22), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 356 TYR 0.014 0.001 TYR A 14 PHE 0.019 0.002 PHE A 370 TRP 0.018 0.001 TRP B 332 HIS 0.003 0.001 HIS B 545 Details of bonding type rmsd covalent geometry : bond 0.00319 (13462) covalent geometry : angle 0.53776 (18206) hydrogen bonds : bond 0.04570 ( 577) hydrogen bonds : angle 5.63578 ( 1623) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 0.403 Fit side-chains REVERT: A 91 ARG cc_start: 0.9090 (OUTLIER) cc_final: 0.8292 (mtt180) REVERT: A 160 ASP cc_start: 0.8575 (t70) cc_final: 0.8305 (t70) REVERT: A 258 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8322 (mt-10) REVERT: A 270 ASP cc_start: 0.8652 (m-30) cc_final: 0.8398 (m-30) REVERT: A 380 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7635 (tt0) REVERT: A 538 GLU cc_start: 0.7908 (mp0) cc_final: 0.7650 (mp0) REVERT: B 91 ARG cc_start: 0.9048 (OUTLIER) cc_final: 0.8153 (mtt180) REVERT: B 138 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8183 (mt-10) REVERT: B 258 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8364 (mt-10) REVERT: B 380 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7625 (tt0) outliers start: 25 outliers final: 17 residues processed: 147 average time/residue: 0.7224 time to fit residues: 113.6065 Evaluate side-chains 150 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 380 GLU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 524 LYS Chi-restraints excluded: chain A residue 737 LYS Chi-restraints excluded: chain A residue 790 GLU Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 792 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 114 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 142 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 139 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.099539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.087307 restraints weight = 14320.808| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 1.27 r_work: 0.2917 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.0639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13462 Z= 0.135 Angle : 0.530 5.496 18206 Z= 0.296 Chirality : 0.046 0.142 1858 Planarity : 0.004 0.043 2372 Dihedral : 6.203 57.558 1807 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.59 % Allowed : 16.18 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.21), residues: 1618 helix: 1.29 (0.24), residues: 478 sheet: 1.36 (0.30), residues: 272 loop : -0.24 (0.22), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 356 TYR 0.014 0.001 TYR A 14 PHE 0.020 0.002 PHE B 370 TRP 0.017 0.001 TRP B 332 HIS 0.003 0.001 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.00299 (13462) covalent geometry : angle 0.52977 (18206) hydrogen bonds : bond 0.04424 ( 577) hydrogen bonds : angle 5.58195 ( 1623) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 0.341 Fit side-chains REVERT: A 91 ARG cc_start: 0.9087 (OUTLIER) cc_final: 0.8288 (mtt180) REVERT: A 160 ASP cc_start: 0.8574 (t70) cc_final: 0.8312 (t70) REVERT: A 258 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8329 (mt-10) REVERT: A 270 ASP cc_start: 0.8654 (m-30) cc_final: 0.8392 (m-30) REVERT: A 538 GLU cc_start: 0.7883 (mp0) cc_final: 0.7621 (mp0) REVERT: B 138 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8164 (mt-10) REVERT: B 258 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.8365 (mt-10) outliers start: 22 outliers final: 16 residues processed: 144 average time/residue: 0.7604 time to fit residues: 117.2127 Evaluate side-chains 147 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 524 LYS Chi-restraints excluded: chain A residue 737 LYS Chi-restraints excluded: chain A residue 790 GLU Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 792 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 59 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 71 optimal weight: 4.9990 chunk 110 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 139 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.099338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.087081 restraints weight = 14346.072| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 1.27 r_work: 0.2912 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.0651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13462 Z= 0.145 Angle : 0.541 5.439 18206 Z= 0.302 Chirality : 0.046 0.143 1858 Planarity : 0.004 0.042 2372 Dihedral : 6.231 57.106 1807 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.73 % Allowed : 16.18 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.21), residues: 1618 helix: 1.26 (0.23), residues: 478 sheet: 1.35 (0.30), residues: 272 loop : -0.25 (0.22), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 356 TYR 0.014 0.001 TYR A 14 PHE 0.020 0.002 PHE B 370 TRP 0.017 0.001 TRP B 332 HIS 0.003 0.001 HIS B 545 Details of bonding type rmsd covalent geometry : bond 0.00324 (13462) covalent geometry : angle 0.54054 (18206) hydrogen bonds : bond 0.04547 ( 577) hydrogen bonds : angle 5.60143 ( 1623) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4470.59 seconds wall clock time: 76 minutes 54.96 seconds (4614.96 seconds total)