Starting phenix.real_space_refine on Sat Aug 23 05:11:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wto_37838/08_2025/8wto_37838.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wto_37838/08_2025/8wto_37838.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wto_37838/08_2025/8wto_37838.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wto_37838/08_2025/8wto_37838.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wto_37838/08_2025/8wto_37838.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wto_37838/08_2025/8wto_37838.map" } resolution = 2.38 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= 0.150 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 64 atoms to isotropic. 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: 8 Type Number sf(0) Gaussians P 4 5.49 5 Mg 2 5.21 5 S 42 5.16 5 Be 2 3.05 5 C 6394 2.51 5 N 1670 2.21 5 O 1760 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 65 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: 9880 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 624, 4906 Classifications: {'peptide': 624} Link IDs: {'PTRANS': 23, 'TRANS': 600} Chain breaks: 3 Chain: "B" Number of atoms: 4906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 624, 4906 Classifications: {'peptide': 624} Link IDs: {'PTRANS': 23, 'TRANS': 600} Chain breaks: 3 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 2.56, per 1000 atoms: 0.26 Number of scatterers: 9880 At special positions: 0 Unit cell: (94.132, 81.084, 141.664, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 42 16.00 P 4 15.00 Mg 2 11.99 F 6 9.00 O 1760 8.00 N 1670 7.00 C 6394 6.00 Be 2 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 646 " - pdb=" SG CYS A 687 " distance=2.03 Simple disulfide: pdb=" SG CYS B 646 " - pdb=" SG CYS B 687 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.98 Conformation dependent library (CDL) restraints added in 437.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2308 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 6 sheets defined 61.5% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 130 through 139 Processing helix chain 'A' and resid 159 through 166 removed outlier: 3.959A pdb=" N VAL A 165 " --> pdb=" O ARG A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 194 Processing helix chain 'A' and resid 199 through 215 Processing helix chain 'A' and resid 233 through 247 removed outlier: 3.833A pdb=" N ASP A 245 " --> pdb=" O SER A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 280 Processing helix chain 'A' and resid 292 through 297 Processing helix chain 'A' and resid 315 through 317 No H-bonds generated for 'chain 'A' and resid 315 through 317' Processing helix chain 'A' and resid 318 through 327 Processing helix chain 'A' and resid 335 through 349 Processing helix chain 'A' and resid 354 through 368 removed outlier: 3.519A pdb=" N LYS A 368 " --> pdb=" O TRP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 397 Processing helix chain 'A' and resid 427 through 445 Processing helix chain 'A' and resid 447 through 468 Processing helix chain 'A' and resid 474 through 496 Processing helix chain 'A' and resid 499 through 505 removed outlier: 4.416A pdb=" N PHE A 503 " --> pdb=" O ALA A 499 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU A 504 " --> pdb=" O LEU A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 515 Processing helix chain 'A' and resid 520 through 532 removed outlier: 3.538A pdb=" N THR A 532 " --> pdb=" O HIS A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 552 removed outlier: 4.848A pdb=" N TRP A 549 " --> pdb=" O VAL A 545 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N ALA A 550 " --> pdb=" O THR A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 583 Processing helix chain 'A' and resid 587 through 605 Processing helix chain 'A' and resid 616 through 618 No H-bonds generated for 'chain 'A' and resid 616 through 618' Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 628 through 640 Processing helix chain 'A' and resid 651 through 655 removed outlier: 3.882A pdb=" N PHE A 654 " --> pdb=" O VAL A 651 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASP A 655 " --> pdb=" O GLN A 652 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 651 through 655' Processing helix chain 'A' and resid 663 through 679 removed outlier: 3.944A pdb=" N SER A 677 " --> pdb=" O SER A 673 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE A 678 " --> pdb=" O VAL A 674 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLY A 679 " --> pdb=" O SER A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 699 Processing helix chain 'A' and resid 704 through 730 Processing helix chain 'B' and resid 130 through 139 Processing helix chain 'B' and resid 159 through 166 removed outlier: 3.539A pdb=" N LYS B 164 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL B 165 " --> pdb=" O ARG B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 194 Processing helix chain 'B' and resid 199 through 215 Processing helix chain 'B' and resid 233 through 246 removed outlier: 3.846A pdb=" N ASP B 245 " --> pdb=" O SER B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 280 Processing helix chain 'B' and resid 292 through 297 Processing helix chain 'B' and resid 318 through 327 Processing helix chain 'B' and resid 335 through 349 Processing helix chain 'B' and resid 354 through 368 removed outlier: 3.795A pdb=" N LYS B 368 " --> pdb=" O TRP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 397 Processing helix chain 'B' and resid 427 through 446 removed outlier: 3.604A pdb=" N GLN B 446 " --> pdb=" O ASN B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 468 Processing helix chain 'B' and resid 474 through 496 Processing helix chain 'B' and resid 499 through 505 removed outlier: 4.416A pdb=" N PHE B 503 " --> pdb=" O ALA B 499 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU B 504 " --> pdb=" O LEU B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 515 Processing helix chain 'B' and resid 520 through 532 removed outlier: 3.539A pdb=" N THR B 532 " --> pdb=" O HIS B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 552 removed outlier: 4.849A pdb=" N TRP B 549 " --> pdb=" O VAL B 545 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ALA B 550 " --> pdb=" O THR B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 585 Processing helix chain 'B' and resid 587 through 605 Processing helix chain 'B' and resid 616 through 618 No H-bonds generated for 'chain 'B' and resid 616 through 618' Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 628 through 640 Processing helix chain 'B' and resid 651 through 655 removed outlier: 3.894A pdb=" N PHE B 654 " --> pdb=" O VAL B 651 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP B 655 " --> pdb=" O GLN B 652 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 651 through 655' Processing helix chain 'B' and resid 663 through 679 removed outlier: 3.979A pdb=" N SER B 677 " --> pdb=" O SER B 673 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE B 678 " --> pdb=" O VAL B 674 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLY B 679 " --> pdb=" O SER B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 698 Processing helix chain 'B' and resid 704 through 730 Processing sheet with id=AA1, first strand: chain 'A' and resid 103 through 116 removed outlier: 3.602A pdb=" N LYS A 103 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N TYR A 80 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP A 109 " --> pdb=" O LEU A 78 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU A 78 " --> pdb=" O ASP A 109 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE A 111 " --> pdb=" O ASN A 76 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ASN A 76 " --> pdb=" O ILE A 111 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N GLY A 113 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N SER A 74 " --> pdb=" O GLY A 113 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N THR A 115 " --> pdb=" O VAL A 72 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL A 72 " --> pdb=" O THR A 115 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU A 78 " --> pdb=" O LYS A 148 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LYS A 148 " --> pdb=" O LEU A 78 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 167 through 170 removed outlier: 6.253A pdb=" N LEU A 253 " --> pdb=" O ILE A 285 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N SER A 287 " --> pdb=" O LEU A 253 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N LEU A 255 " --> pdb=" O SER A 287 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE A 312 " --> pdb=" O PHE A 304 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N SER A 306 " --> pdb=" O THR A 310 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N THR A 310 " --> pdb=" O SER A 306 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 646 through 649 removed outlier: 6.574A pdb=" N CYS A 646 " --> pdb=" O THR A 690 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N THR A 690 " --> pdb=" O CYS A 646 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL A 648 " --> pdb=" O LEU A 688 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 103 through 116 removed outlier: 3.602A pdb=" N LYS B 103 " --> pdb=" O VAL B 84 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N TYR B 80 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASP B 109 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU B 78 " --> pdb=" O ASP B 109 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE B 111 " --> pdb=" O ASN B 76 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ASN B 76 " --> pdb=" O ILE B 111 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLY B 113 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N SER B 74 " --> pdb=" O GLY B 113 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N THR B 115 " --> pdb=" O VAL B 72 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N VAL B 72 " --> pdb=" O THR B 115 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU B 78 " --> pdb=" O LYS B 148 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LYS B 148 " --> pdb=" O LEU B 78 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 167 through 170 removed outlier: 6.247A pdb=" N LEU B 253 " --> pdb=" O ILE B 285 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N SER B 287 " --> pdb=" O LEU B 253 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N LEU B 255 " --> pdb=" O SER B 287 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE B 312 " --> pdb=" O PHE B 304 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N SER B 306 " --> pdb=" O THR B 310 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N THR B 310 " --> pdb=" O SER B 306 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 646 through 649 removed outlier: 6.550A pdb=" N CYS B 646 " --> pdb=" O THR B 690 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N THR B 690 " --> pdb=" O CYS B 646 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL B 648 " --> pdb=" O LEU B 688 " (cutoff:3.500A) 575 hydrogen bonds defined for protein. 1713 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.72 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 1522 1.27 - 1.41: 2568 1.41 - 1.54: 5759 1.54 - 1.67: 161 1.67 - 1.81: 74 Bond restraints: 10084 Sorted by residual: bond pdb=" C2' ADP B 801 " pdb=" C3' ADP B 801 " ideal model delta sigma weight residual 1.524 1.243 0.281 2.00e-02 2.50e+03 1.97e+02 bond pdb=" C2' ADP A 801 " pdb=" C3' ADP A 801 " ideal model delta sigma weight residual 1.524 1.243 0.281 2.00e-02 2.50e+03 1.97e+02 bond pdb=" CA ASP A 173 " pdb=" C ASP A 173 " ideal model delta sigma weight residual 1.523 1.404 0.119 1.24e-02 6.50e+03 9.20e+01 bond pdb=" CA ASP B 173 " pdb=" C ASP B 173 " ideal model delta sigma weight residual 1.523 1.404 0.119 1.24e-02 6.50e+03 9.14e+01 bond pdb=" C4 ADP B 801 " pdb=" C5 ADP B 801 " ideal model delta sigma weight residual 1.490 1.313 0.177 2.00e-02 2.50e+03 7.87e+01 ... (remaining 10079 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.07: 13582 5.07 - 10.14: 42 10.14 - 15.20: 16 15.20 - 20.27: 0 20.27 - 25.34: 4 Bond angle restraints: 13644 Sorted by residual: angle pdb=" C1' ADP A 801 " pdb=" N9 ADP A 801 " pdb=" C4 ADP A 801 " ideal model delta sigma weight residual 126.00 151.34 -25.34 3.00e+00 1.11e-01 7.13e+01 angle pdb=" C1' ADP B 801 " pdb=" N9 ADP B 801 " pdb=" C4 ADP B 801 " ideal model delta sigma weight residual 126.00 151.33 -25.33 3.00e+00 1.11e-01 7.13e+01 angle pdb=" C1' ADP B 801 " pdb=" N9 ADP B 801 " pdb=" C8 ADP B 801 " ideal model delta sigma weight residual 126.00 101.34 24.66 3.00e+00 1.11e-01 6.76e+01 angle pdb=" C1' ADP A 801 " pdb=" N9 ADP A 801 " pdb=" C8 ADP A 801 " ideal model delta sigma weight residual 126.00 101.34 24.66 3.00e+00 1.11e-01 6.76e+01 angle pdb=" N ASP B 173 " pdb=" CA ASP B 173 " pdb=" C ASP B 173 " ideal model delta sigma weight residual 109.76 118.81 -9.05 1.64e+00 3.72e-01 3.04e+01 ... (remaining 13639 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.31: 5803 29.31 - 58.61: 153 58.61 - 87.91: 20 87.91 - 117.22: 0 117.22 - 146.52: 2 Dihedral angle restraints: 5978 sinusoidal: 2398 harmonic: 3580 Sorted by residual: dihedral pdb=" C5' ADP A 801 " pdb=" O5' ADP A 801 " pdb=" PA ADP A 801 " pdb=" O2A ADP A 801 " ideal model delta sinusoidal sigma weight residual 300.00 153.48 146.52 1 2.00e+01 2.50e-03 4.40e+01 dihedral pdb=" C5' ADP B 801 " pdb=" O5' ADP B 801 " pdb=" PA ADP B 801 " pdb=" O2A ADP B 801 " ideal model delta sinusoidal sigma weight residual 300.00 153.56 146.44 1 2.00e+01 2.50e-03 4.40e+01 dihedral pdb=" CB CYS B 646 " pdb=" SG CYS B 646 " pdb=" SG CYS B 687 " pdb=" CB CYS B 687 " ideal model delta sinusoidal sigma weight residual -86.00 -134.09 48.09 1 1.00e+01 1.00e-02 3.19e+01 ... (remaining 5975 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 1432 0.090 - 0.179: 134 0.179 - 0.269: 4 0.269 - 0.359: 0 0.359 - 0.448: 4 Chirality restraints: 1574 Sorted by residual: chirality pdb=" CA ASP B 173 " pdb=" N ASP B 173 " pdb=" C ASP B 173 " pdb=" CB ASP B 173 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.02e+00 chirality pdb=" CA ASP A 173 " pdb=" N ASP A 173 " pdb=" C ASP A 173 " pdb=" CB ASP A 173 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.00e+00 chirality pdb=" CA GLN B 172 " pdb=" N GLN B 172 " pdb=" C GLN B 172 " pdb=" CB GLN B 172 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.67e+00 ... (remaining 1571 not shown) Planarity restraints: 1692 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN B 172 " 0.013 2.00e-02 2.50e+03 2.65e-02 7.04e+00 pdb=" C GLN B 172 " -0.046 2.00e-02 2.50e+03 pdb=" O GLN B 172 " 0.018 2.00e-02 2.50e+03 pdb=" N ASP B 173 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 172 " -0.013 2.00e-02 2.50e+03 2.63e-02 6.93e+00 pdb=" C GLN A 172 " 0.046 2.00e-02 2.50e+03 pdb=" O GLN A 172 " -0.018 2.00e-02 2.50e+03 pdb=" N ASP A 173 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR B 630 " 0.036 5.00e-02 4.00e+02 5.42e-02 4.69e+00 pdb=" N PRO B 631 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO B 631 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 631 " 0.031 5.00e-02 4.00e+02 ... (remaining 1689 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 114 2.64 - 3.21: 8383 3.21 - 3.77: 16244 3.77 - 4.34: 23048 4.34 - 4.90: 36237 Nonbonded interactions: 84026 Sorted by model distance: nonbonded pdb="MG MG B 803 " pdb=" O HOH B 902 " model vdw 2.081 2.170 nonbonded pdb="MG MG A 803 " pdb=" O HOH A 902 " model vdw 2.081 2.170 nonbonded pdb=" O2B ADP B 801 " pdb="MG MG B 803 " model vdw 2.166 2.170 nonbonded pdb=" O2B ADP A 801 " pdb="MG MG A 803 " model vdw 2.168 2.170 nonbonded pdb=" OE2 GLU B 257 " pdb=" O HOH B 901 " model vdw 2.275 3.040 ... (remaining 84021 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: 1.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.290 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 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 : 0.016 0.899 10088 Z= 1.362 Angle : 1.043 25.339 13648 Z= 0.508 Chirality : 0.057 0.448 1574 Planarity : 0.006 0.054 1692 Dihedral : 14.488 146.524 3664 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.83 (0.17), residues: 1232 helix: -3.01 (0.11), residues: 744 sheet: -0.50 (0.47), residues: 86 loop : -1.56 (0.28), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 238 TYR 0.024 0.003 TYR A 516 PHE 0.032 0.003 PHE B 608 TRP 0.014 0.002 TRP A 621 HIS 0.012 0.003 HIS A 248 Details of bonding type rmsd covalent geometry : bond 0.00986 (10084) covalent geometry : angle 1.04191 (13644) SS BOND : bond 0.00165 ( 2) SS BOND : angle 2.37540 ( 4) hydrogen bonds : bond 0.24404 ( 575) hydrogen bonds : angle 8.17897 ( 1713) Misc. bond : bond 0.89865 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.418 Fit side-chains REVERT: A 359 GLU cc_start: 0.7243 (mm-30) cc_final: 0.6891 (mm-30) REVERT: A 364 TRP cc_start: 0.8448 (t-100) cc_final: 0.8095 (t-100) REVERT: A 682 ILE cc_start: 0.8785 (mt) cc_final: 0.8415 (mp) REVERT: B 359 GLU cc_start: 0.7240 (mm-30) cc_final: 0.6856 (mm-30) REVERT: B 362 LYS cc_start: 0.8086 (mttt) cc_final: 0.7849 (mttt) REVERT: B 682 ILE cc_start: 0.8835 (mt) cc_final: 0.8461 (mp) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.8491 time to fit residues: 160.0382 Evaluate side-chains 141 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 0.5980 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 123 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN A 335 ASN A 473 ASN A 652 GLN B 140 ASN B 370 GLN B 473 ASN B 652 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.145349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.106525 restraints weight = 8788.259| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 1.41 r_work: 0.3028 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10088 Z= 0.141 Angle : 0.578 7.013 13648 Z= 0.293 Chirality : 0.041 0.142 1574 Planarity : 0.005 0.033 1692 Dihedral : 7.318 126.098 1372 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.58 % Allowed : 9.50 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.22), residues: 1232 helix: -0.01 (0.17), residues: 742 sheet: -0.14 (0.48), residues: 86 loop : -1.09 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 161 TYR 0.026 0.002 TYR A 592 PHE 0.021 0.002 PHE A 608 TRP 0.014 0.002 TRP B 429 HIS 0.004 0.001 HIS B 248 Details of bonding type rmsd covalent geometry : bond 0.00313 (10084) covalent geometry : angle 0.57755 (13644) SS BOND : bond 0.00029 ( 2) SS BOND : angle 1.04906 ( 4) hydrogen bonds : bond 0.04522 ( 575) hydrogen bonds : angle 4.27693 ( 1713) Misc. bond : bond 0.00103 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 137 time to evaluate : 0.428 Fit side-chains REVERT: A 272 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.8313 (mtmm) REVERT: A 348 GLU cc_start: 0.6962 (mt-10) cc_final: 0.6535 (mt-10) REVERT: A 359 GLU cc_start: 0.6870 (mm-30) cc_final: 0.6121 (mt-10) REVERT: A 666 MET cc_start: 0.7731 (tpp) cc_final: 0.7529 (tpp) REVERT: A 682 ILE cc_start: 0.8569 (mt) cc_final: 0.8181 (mp) REVERT: B 272 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8293 (mtmm) REVERT: B 348 GLU cc_start: 0.6966 (mt-10) cc_final: 0.6541 (mt-10) REVERT: B 359 GLU cc_start: 0.6933 (mm-30) cc_final: 0.6213 (mt-10) REVERT: B 362 LYS cc_start: 0.7169 (mttt) cc_final: 0.6927 (mttt) REVERT: B 398 ARG cc_start: 0.7606 (ttm-80) cc_final: 0.7347 (mmt-90) REVERT: B 682 ILE cc_start: 0.8533 (mt) cc_final: 0.8140 (mp) REVERT: B 697 GLN cc_start: 0.8418 (mt0) cc_final: 0.8199 (mt0) outliers start: 17 outliers final: 10 residues processed: 146 average time/residue: 0.8323 time to fit residues: 128.3075 Evaluate side-chains 138 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 126 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 LYS Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain B residue 272 LYS Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 651 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 89 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 76 optimal weight: 0.0970 chunk 94 optimal weight: 4.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 587 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 = 0.3558 r_free = 0.3558 target = 0.140689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.100681 restraints weight = 8797.434| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 1.47 r_work: 0.2949 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.040 10088 Z= 0.295 Angle : 0.709 9.048 13648 Z= 0.361 Chirality : 0.051 0.173 1574 Planarity : 0.006 0.071 1692 Dihedral : 7.671 128.025 1372 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.51 % Allowed : 10.52 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.23), residues: 1232 helix: 0.71 (0.18), residues: 744 sheet: -0.01 (0.49), residues: 86 loop : -0.96 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 239 TYR 0.034 0.003 TYR A 592 PHE 0.030 0.003 PHE A 608 TRP 0.011 0.002 TRP A 621 HIS 0.007 0.002 HIS A 248 Details of bonding type rmsd covalent geometry : bond 0.00697 (10084) covalent geometry : angle 0.70863 (13644) SS BOND : bond 0.00081 ( 2) SS BOND : angle 1.27674 ( 4) hydrogen bonds : bond 0.05864 ( 575) hydrogen bonds : angle 4.30363 ( 1713) Misc. bond : bond 0.00075 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 127 time to evaluate : 0.383 Fit side-chains REVERT: A 359 GLU cc_start: 0.6833 (mm-30) cc_final: 0.6069 (mt-10) REVERT: A 505 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.8119 (mt0) REVERT: A 682 ILE cc_start: 0.8553 (mt) cc_final: 0.8160 (mp) REVERT: B 359 GLU cc_start: 0.6815 (mm-30) cc_final: 0.6019 (mt-10) REVERT: B 362 LYS cc_start: 0.7134 (mttt) cc_final: 0.6876 (mttt) REVERT: B 398 ARG cc_start: 0.7580 (ttm-80) cc_final: 0.7189 (mmt-90) REVERT: B 505 GLN cc_start: 0.8393 (OUTLIER) cc_final: 0.8120 (mt0) REVERT: B 682 ILE cc_start: 0.8559 (mt) cc_final: 0.8129 (mp) outliers start: 27 outliers final: 16 residues processed: 140 average time/residue: 0.8549 time to fit residues: 126.1823 Evaluate side-chains 143 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 505 GLN Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 505 GLN Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 651 VAL Chi-restraints excluded: chain B residue 672 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 80 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 73 optimal weight: 0.0570 chunk 6 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 overall best weight: 0.7702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 587 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 = 0.3618 r_free = 0.3618 target = 0.145926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.105908 restraints weight = 8923.430| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 1.51 r_work: 0.3019 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10088 Z= 0.116 Angle : 0.525 6.854 13648 Z= 0.263 Chirality : 0.040 0.145 1574 Planarity : 0.004 0.032 1692 Dihedral : 7.097 126.274 1372 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.23 % Allowed : 10.89 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.24), residues: 1232 helix: 1.47 (0.19), residues: 744 sheet: 0.06 (0.49), residues: 86 loop : -0.79 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 161 TYR 0.024 0.002 TYR A 592 PHE 0.019 0.001 PHE A 608 TRP 0.011 0.001 TRP B 429 HIS 0.003 0.001 HIS A 248 Details of bonding type rmsd covalent geometry : bond 0.00254 (10084) covalent geometry : angle 0.52548 (13644) SS BOND : bond 0.00083 ( 2) SS BOND : angle 0.47941 ( 4) hydrogen bonds : bond 0.03885 ( 575) hydrogen bonds : angle 3.84173 ( 1713) Misc. bond : bond 0.00110 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 138 time to evaluate : 0.411 Fit side-chains REVERT: A 272 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8209 (mtmm) REVERT: A 359 GLU cc_start: 0.6844 (mm-30) cc_final: 0.6081 (mt-10) REVERT: A 397 SER cc_start: 0.8022 (OUTLIER) cc_final: 0.7776 (p) REVERT: A 429 TRP cc_start: 0.8447 (OUTLIER) cc_final: 0.8236 (p90) REVERT: A 505 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.8074 (mt0) REVERT: A 620 ILE cc_start: 0.8673 (mm) cc_final: 0.8462 (mm) REVERT: A 682 ILE cc_start: 0.8540 (mt) cc_final: 0.8152 (mp) REVERT: B 272 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8199 (mtmm) REVERT: B 359 GLU cc_start: 0.6844 (mm-30) cc_final: 0.6082 (mt-10) REVERT: B 362 LYS cc_start: 0.7095 (mttt) cc_final: 0.6825 (mttt) REVERT: B 429 TRP cc_start: 0.8446 (OUTLIER) cc_final: 0.8233 (p90) REVERT: B 505 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.8068 (mt0) REVERT: B 620 ILE cc_start: 0.8661 (mm) cc_final: 0.8451 (mm) REVERT: B 682 ILE cc_start: 0.8513 (mt) cc_final: 0.8098 (mp) outliers start: 24 outliers final: 9 residues processed: 153 average time/residue: 0.7478 time to fit residues: 121.2943 Evaluate side-chains 144 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 272 LYS Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 429 TRP Chi-restraints excluded: chain A residue 505 GLN Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 272 LYS Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 429 TRP Chi-restraints excluded: chain B residue 505 GLN Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 628 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 89 optimal weight: 9.9990 chunk 115 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 106 optimal weight: 7.9990 chunk 111 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 57 optimal weight: 10.0000 chunk 85 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 442 ASN ** B 587 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 = 0.3584 r_free = 0.3584 target = 0.142974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.102742 restraints weight = 8850.759| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.49 r_work: 0.2975 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 10088 Z= 0.197 Angle : 0.609 8.196 13648 Z= 0.308 Chirality : 0.045 0.148 1574 Planarity : 0.004 0.039 1692 Dihedral : 7.374 127.111 1372 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.61 % Allowed : 11.36 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.23), residues: 1232 helix: 1.50 (0.19), residues: 746 sheet: -0.01 (0.47), residues: 86 loop : -0.73 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 161 TYR 0.035 0.002 TYR A 592 PHE 0.024 0.002 PHE A 608 TRP 0.011 0.002 TRP A 429 HIS 0.005 0.001 HIS B 248 Details of bonding type rmsd covalent geometry : bond 0.00459 (10084) covalent geometry : angle 0.60910 (13644) SS BOND : bond 0.00043 ( 2) SS BOND : angle 0.62986 ( 4) hydrogen bonds : bond 0.04777 ( 575) hydrogen bonds : angle 3.97540 ( 1713) Misc. bond : bond 0.00146 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 134 time to evaluate : 0.388 Fit side-chains REVERT: A 272 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8228 (mtmm) REVERT: A 359 GLU cc_start: 0.6812 (mm-30) cc_final: 0.5984 (mt-10) REVERT: A 397 SER cc_start: 0.8082 (OUTLIER) cc_final: 0.7822 (p) REVERT: A 505 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.8102 (mt0) REVERT: A 620 ILE cc_start: 0.8691 (mm) cc_final: 0.8471 (mm) REVERT: A 682 ILE cc_start: 0.8526 (mt) cc_final: 0.8146 (mp) REVERT: B 272 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8211 (mtmm) REVERT: B 359 GLU cc_start: 0.6871 (mm-30) cc_final: 0.6082 (mt-10) REVERT: B 362 LYS cc_start: 0.7148 (mttt) cc_final: 0.5391 (mmtm) REVERT: B 505 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.8094 (mt0) REVERT: B 620 ILE cc_start: 0.8690 (mm) cc_final: 0.8471 (mm) REVERT: B 682 ILE cc_start: 0.8504 (mt) cc_final: 0.8088 (mp) outliers start: 28 outliers final: 17 residues processed: 151 average time/residue: 0.7446 time to fit residues: 118.7825 Evaluate side-chains 151 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 272 LYS Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 505 GLN Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 672 ASP Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 272 LYS Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 505 GLN Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 651 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 44 optimal weight: 6.9990 chunk 71 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 115 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 117 optimal weight: 0.3980 chunk 24 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 442 ASN ** A 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 587 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 = 0.3583 r_free = 0.3583 target = 0.143006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.102843 restraints weight = 8875.553| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 1.50 r_work: 0.2972 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10088 Z= 0.191 Angle : 0.600 8.011 13648 Z= 0.303 Chirality : 0.045 0.187 1574 Planarity : 0.004 0.035 1692 Dihedral : 7.327 126.852 1372 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.70 % Allowed : 11.92 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.23), residues: 1232 helix: 1.59 (0.18), residues: 746 sheet: -0.02 (0.47), residues: 86 loop : -0.67 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 161 TYR 0.037 0.003 TYR A 592 PHE 0.023 0.002 PHE B 608 TRP 0.009 0.002 TRP A 364 HIS 0.004 0.001 HIS B 248 Details of bonding type rmsd covalent geometry : bond 0.00447 (10084) covalent geometry : angle 0.60038 (13644) SS BOND : bond 0.00010 ( 2) SS BOND : angle 0.54156 ( 4) hydrogen bonds : bond 0.04664 ( 575) hydrogen bonds : angle 3.93223 ( 1713) Misc. bond : bond 0.00186 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 130 time to evaluate : 0.403 Fit side-chains REVERT: A 272 LYS cc_start: 0.8652 (OUTLIER) cc_final: 0.8204 (mtmm) REVERT: A 359 GLU cc_start: 0.6802 (mm-30) cc_final: 0.5968 (mt-10) REVERT: A 397 SER cc_start: 0.8020 (OUTLIER) cc_final: 0.7762 (p) REVERT: A 505 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.8078 (mt0) REVERT: A 609 PHE cc_start: 0.7791 (OUTLIER) cc_final: 0.7341 (t80) REVERT: A 620 ILE cc_start: 0.8681 (mm) cc_final: 0.8464 (mm) REVERT: A 682 ILE cc_start: 0.8518 (mt) cc_final: 0.8120 (mp) REVERT: B 272 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8196 (mtmm) REVERT: B 359 GLU cc_start: 0.6858 (mm-30) cc_final: 0.6030 (mt-10) REVERT: B 362 LYS cc_start: 0.7136 (mttt) cc_final: 0.5388 (mmtm) REVERT: B 505 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.8072 (mt0) REVERT: B 609 PHE cc_start: 0.7775 (OUTLIER) cc_final: 0.7324 (t80) REVERT: B 620 ILE cc_start: 0.8681 (mm) cc_final: 0.8466 (mm) REVERT: B 682 ILE cc_start: 0.8503 (mt) cc_final: 0.8093 (mp) outliers start: 29 outliers final: 18 residues processed: 145 average time/residue: 0.8044 time to fit residues: 123.3334 Evaluate side-chains 152 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 272 LYS Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 505 GLN Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 609 PHE Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 272 LYS Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 505 GLN Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 609 PHE Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 651 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 31 optimal weight: 0.5980 chunk 86 optimal weight: 10.0000 chunk 75 optimal weight: 5.9990 chunk 68 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 84 optimal weight: 5.9990 chunk 102 optimal weight: 0.6980 chunk 50 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 587 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 = 0.3598 r_free = 0.3598 target = 0.144290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.105041 restraints weight = 8884.471| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 1.45 r_work: 0.3015 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10088 Z= 0.127 Angle : 0.537 7.201 13648 Z= 0.268 Chirality : 0.041 0.174 1574 Planarity : 0.004 0.033 1692 Dihedral : 7.090 126.452 1372 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.61 % Allowed : 12.48 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.40 (0.24), residues: 1232 helix: 1.86 (0.19), residues: 744 sheet: 0.08 (0.46), residues: 86 loop : -0.63 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 161 TYR 0.033 0.002 TYR A 592 PHE 0.019 0.001 PHE B 608 TRP 0.009 0.001 TRP B 572 HIS 0.003 0.001 HIS B 248 Details of bonding type rmsd covalent geometry : bond 0.00286 (10084) covalent geometry : angle 0.53732 (13644) SS BOND : bond 0.00043 ( 2) SS BOND : angle 0.39088 ( 4) hydrogen bonds : bond 0.03945 ( 575) hydrogen bonds : angle 3.76141 ( 1713) Misc. bond : bond 0.00120 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 137 time to evaluate : 0.324 Fit side-chains REVERT: A 272 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8224 (mtmm) REVERT: A 359 GLU cc_start: 0.6919 (mm-30) cc_final: 0.6100 (mt-10) REVERT: A 397 SER cc_start: 0.8011 (OUTLIER) cc_final: 0.7772 (p) REVERT: A 505 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.8078 (mt0) REVERT: A 609 PHE cc_start: 0.7764 (OUTLIER) cc_final: 0.7310 (t80) REVERT: A 682 ILE cc_start: 0.8601 (mt) cc_final: 0.8193 (mp) REVERT: B 272 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8211 (mtmm) REVERT: B 359 GLU cc_start: 0.6913 (mm-30) cc_final: 0.6086 (mt-10) REVERT: B 362 LYS cc_start: 0.7229 (mttt) cc_final: 0.6997 (mtpt) REVERT: B 505 GLN cc_start: 0.8338 (OUTLIER) cc_final: 0.8064 (mt0) REVERT: B 609 PHE cc_start: 0.7768 (OUTLIER) cc_final: 0.7310 (t80) outliers start: 28 outliers final: 17 residues processed: 156 average time/residue: 0.7757 time to fit residues: 128.2563 Evaluate side-chains 147 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 272 LYS Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 505 GLN Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 609 PHE Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 272 LYS Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 505 GLN Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 609 PHE Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 651 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 68 optimal weight: 0.3980 chunk 95 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 90 optimal weight: 0.2980 chunk 114 optimal weight: 0.9980 chunk 97 optimal weight: 0.0570 chunk 82 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 587 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 = 0.3634 r_free = 0.3634 target = 0.147507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.108207 restraints weight = 8992.531| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.50 r_work: 0.3050 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 10088 Z= 0.100 Angle : 0.501 6.483 13648 Z= 0.248 Chirality : 0.039 0.148 1574 Planarity : 0.004 0.033 1692 Dihedral : 6.720 121.668 1372 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.05 % Allowed : 12.85 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.76 (0.24), residues: 1232 helix: 2.18 (0.19), residues: 744 sheet: 0.21 (0.46), residues: 86 loop : -0.57 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 161 TYR 0.029 0.002 TYR A 592 PHE 0.016 0.001 PHE B 608 TRP 0.009 0.001 TRP B 572 HIS 0.002 0.001 HIS B 248 Details of bonding type rmsd covalent geometry : bond 0.00217 (10084) covalent geometry : angle 0.50073 (13644) SS BOND : bond 0.00073 ( 2) SS BOND : angle 0.35844 ( 4) hydrogen bonds : bond 0.03459 ( 575) hydrogen bonds : angle 3.57145 ( 1713) Misc. bond : bond 0.00125 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 0.393 Fit side-chains REVERT: A 359 GLU cc_start: 0.6861 (mm-30) cc_final: 0.6048 (mt-10) REVERT: A 397 SER cc_start: 0.7982 (OUTLIER) cc_final: 0.7757 (p) REVERT: A 505 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.8080 (mt0) REVERT: A 682 ILE cc_start: 0.8556 (mt) cc_final: 0.8151 (mp) REVERT: B 362 LYS cc_start: 0.7176 (mttt) cc_final: 0.6914 (mtpt) REVERT: B 505 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.8063 (mt0) outliers start: 22 outliers final: 9 residues processed: 143 average time/residue: 0.7776 time to fit residues: 117.8559 Evaluate side-chains 135 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 123 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 505 GLN Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 505 GLN Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 628 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 50 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 12 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 24 optimal weight: 9.9990 chunk 106 optimal weight: 0.8980 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 587 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 = 0.3583 r_free = 0.3583 target = 0.142862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.102673 restraints weight = 8880.180| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 1.49 r_work: 0.2971 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 10088 Z= 0.210 Angle : 0.621 8.333 13648 Z= 0.313 Chirality : 0.046 0.200 1574 Planarity : 0.004 0.041 1692 Dihedral : 7.327 127.566 1372 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.77 % Allowed : 13.59 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (0.24), residues: 1232 helix: 1.78 (0.18), residues: 750 sheet: 0.12 (0.46), residues: 86 loop : -0.63 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 239 TYR 0.052 0.003 TYR A 592 PHE 0.023 0.002 PHE B 608 TRP 0.009 0.002 TRP A 364 HIS 0.004 0.001 HIS A 248 Details of bonding type rmsd covalent geometry : bond 0.00496 (10084) covalent geometry : angle 0.62090 (13644) SS BOND : bond 0.00064 ( 2) SS BOND : angle 0.69182 ( 4) hydrogen bonds : bond 0.04810 ( 575) hydrogen bonds : angle 3.89175 ( 1713) Misc. bond : bond 0.00132 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 0.490 Fit side-chains REVERT: A 359 GLU cc_start: 0.6902 (mm-30) cc_final: 0.6058 (mt-10) REVERT: A 397 SER cc_start: 0.8040 (OUTLIER) cc_final: 0.7785 (p) REVERT: A 505 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.8085 (mt0) REVERT: A 682 ILE cc_start: 0.8544 (mt) cc_final: 0.8151 (mp) REVERT: B 359 GLU cc_start: 0.6836 (mm-30) cc_final: 0.6019 (mt-10) REVERT: B 362 LYS cc_start: 0.7200 (mttt) cc_final: 0.5432 (mmtm) REVERT: B 505 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.8079 (mt0) outliers start: 19 outliers final: 15 residues processed: 136 average time/residue: 0.8334 time to fit residues: 119.7859 Evaluate side-chains 137 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 505 GLN Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 505 GLN Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 651 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 5 optimal weight: 0.7980 chunk 87 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 57 optimal weight: 10.0000 chunk 39 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 89 optimal weight: 10.0000 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 587 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 = 0.3604 r_free = 0.3604 target = 0.144681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.104706 restraints weight = 8792.399| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 1.50 r_work: 0.3003 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10088 Z= 0.136 Angle : 0.549 7.371 13648 Z= 0.274 Chirality : 0.042 0.175 1574 Planarity : 0.004 0.034 1692 Dihedral : 7.113 126.920 1372 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.68 % Allowed : 13.41 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.49 (0.24), residues: 1232 helix: 1.93 (0.19), residues: 748 sheet: 0.12 (0.46), residues: 86 loop : -0.61 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 161 TYR 0.042 0.002 TYR A 592 PHE 0.019 0.002 PHE A 608 TRP 0.009 0.001 TRP B 572 HIS 0.003 0.001 HIS A 248 Details of bonding type rmsd covalent geometry : bond 0.00311 (10084) covalent geometry : angle 0.54940 (13644) SS BOND : bond 0.00030 ( 2) SS BOND : angle 0.68269 ( 4) hydrogen bonds : bond 0.04067 ( 575) hydrogen bonds : angle 3.75412 ( 1713) Misc. bond : bond 0.00157 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 0.454 Fit side-chains REVERT: A 359 GLU cc_start: 0.6882 (mm-30) cc_final: 0.6055 (mt-10) REVERT: A 397 SER cc_start: 0.8019 (OUTLIER) cc_final: 0.7764 (p) REVERT: A 505 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.8070 (mt0) REVERT: A 682 ILE cc_start: 0.8543 (mt) cc_final: 0.8137 (mp) REVERT: B 362 LYS cc_start: 0.7212 (mttt) cc_final: 0.6926 (mtpt) REVERT: B 505 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.8078 (mt0) outliers start: 18 outliers final: 14 residues processed: 138 average time/residue: 0.7927 time to fit residues: 115.8281 Evaluate side-chains 140 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 505 GLN Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 505 GLN Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 651 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 4 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 chunk 88 optimal weight: 0.9980 chunk 120 optimal weight: 3.9990 chunk 16 optimal weight: 0.1980 chunk 84 optimal weight: 6.9990 chunk 57 optimal weight: 10.0000 chunk 25 optimal weight: 0.2980 chunk 104 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 587 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 = 0.3593 r_free = 0.3593 target = 0.143748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.104609 restraints weight = 8950.244| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 1.44 r_work: 0.3000 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10088 Z= 0.151 Angle : 0.565 7.669 13648 Z= 0.283 Chirality : 0.043 0.180 1574 Planarity : 0.004 0.034 1692 Dihedral : 7.137 126.158 1372 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.58 % Allowed : 13.87 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.44 (0.24), residues: 1232 helix: 1.88 (0.19), residues: 748 sheet: 0.12 (0.46), residues: 86 loop : -0.61 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 161 TYR 0.047 0.002 TYR A 592 PHE 0.020 0.002 PHE B 608 TRP 0.009 0.001 TRP B 572 HIS 0.004 0.001 HIS B 248 Details of bonding type rmsd covalent geometry : bond 0.00348 (10084) covalent geometry : angle 0.56506 (13644) SS BOND : bond 0.00011 ( 2) SS BOND : angle 0.61418 ( 4) hydrogen bonds : bond 0.04234 ( 575) hydrogen bonds : angle 3.77697 ( 1713) Misc. bond : bond 0.00151 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4411.49 seconds wall clock time: 75 minutes 58.75 seconds (4558.75 seconds total)