Starting phenix.real_space_refine on Tue May 13 08:41:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wto_37838/05_2025/8wto_37838.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wto_37838/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8wto_37838/05_2025/8wto_37838.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wto_37838/05_2025/8wto_37838.map" model { file = "/net/cci-nas-00/data/ceres_data/8wto_37838/05_2025/8wto_37838.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wto_37838/05_2025/8wto_37838.cif" } resolution = 2.38 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 5.62, per 1000 atoms: 0.57 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: 2.25 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.94 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: 2.91 Time building geometry restraints manager: 2.66 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: 0.05 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: 1.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.120 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 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:12.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.290 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.014 0.002 TRP A 621 HIS 0.012 0.003 HIS A 248 PHE 0.032 0.003 PHE B 608 TYR 0.024 0.003 TYR A 516 ARG 0.006 0.001 ARG A 238 Details of bonding type rmsd hydrogen bonds : bond 0.24404 ( 575) hydrogen bonds : angle 8.17897 ( 1713) SS BOND : bond 0.00165 ( 2) SS BOND : angle 2.37540 ( 4) covalent geometry : bond 0.00986 (10084) covalent geometry : angle 1.04191 (13644) 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 : 1.023 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: 1.5469 time to fit residues: 292.3631 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 : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 370 GLN B 473 ASN B 652 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.144520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.105477 restraints weight = 8757.464| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 1.42 r_work: 0.3012 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 10088 Z= 0.157 Angle : 0.595 7.134 13648 Z= 0.303 Chirality : 0.042 0.153 1574 Planarity : 0.005 0.040 1692 Dihedral : 7.479 129.571 1372 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.86 % Allowed : 8.85 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.22), residues: 1232 helix: -0.01 (0.17), residues: 742 sheet: -0.18 (0.47), residues: 86 loop : -1.09 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 429 HIS 0.005 0.001 HIS B 248 PHE 0.023 0.002 PHE B 608 TYR 0.028 0.002 TYR A 592 ARG 0.003 0.000 ARG B 161 Details of bonding type rmsd hydrogen bonds : bond 0.04774 ( 575) hydrogen bonds : angle 4.30608 ( 1713) SS BOND : bond 0.00026 ( 2) SS BOND : angle 1.10701 ( 4) covalent geometry : bond 0.00352 (10084) covalent geometry : angle 0.59462 (13644) Misc. bond : bond 0.00127 ( 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 155 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 135 time to evaluate : 1.188 Fit side-chains REVERT: A 272 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8313 (mtmm) REVERT: A 359 GLU cc_start: 0.6912 (mm-30) cc_final: 0.6185 (mt-10) REVERT: A 666 MET cc_start: 0.7755 (tpp) cc_final: 0.7538 (tpp) REVERT: A 682 ILE cc_start: 0.8582 (mt) cc_final: 0.8195 (mp) REVERT: A 697 GLN cc_start: 0.8416 (mt0) cc_final: 0.8193 (mt0) REVERT: B 272 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8296 (mtmm) REVERT: B 359 GLU cc_start: 0.6899 (mm-30) cc_final: 0.6172 (mt-10) REVERT: B 362 LYS cc_start: 0.7197 (mttt) cc_final: 0.6956 (mttt) REVERT: B 398 ARG cc_start: 0.7604 (ttm-80) cc_final: 0.7343 (mmt-90) REVERT: B 682 ILE cc_start: 0.8559 (mt) cc_final: 0.8154 (mp) REVERT: B 697 GLN cc_start: 0.8438 (mt0) cc_final: 0.8214 (mt0) outliers start: 20 outliers final: 13 residues processed: 144 average time/residue: 1.5082 time to fit residues: 230.1056 Evaluate side-chains 146 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 131 time to evaluate : 1.000 ------------------------------------------------------------------------------- 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 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 104 THR 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 Chi-restraints excluded: chain B residue 672 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 2 optimal weight: 5.9990 chunk 123 optimal weight: 0.0980 chunk 24 optimal weight: 8.9990 chunk 31 optimal weight: 0.6980 chunk 38 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 91 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3622 r_free = 0.3622 target = 0.146258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.106278 restraints weight = 8799.851| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 1.49 r_work: 0.3028 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1693 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= 0.121 Angle : 0.534 7.087 13648 Z= 0.267 Chirality : 0.040 0.144 1574 Planarity : 0.004 0.034 1692 Dihedral : 7.116 126.758 1372 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.96 % Allowed : 10.52 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.23), residues: 1232 helix: 1.15 (0.18), residues: 744 sheet: 0.03 (0.48), residues: 86 loop : -0.88 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 429 HIS 0.004 0.001 HIS B 248 PHE 0.019 0.001 PHE A 608 TYR 0.024 0.002 TYR A 592 ARG 0.004 0.000 ARG A 161 Details of bonding type rmsd hydrogen bonds : bond 0.04081 ( 575) hydrogen bonds : angle 3.92541 ( 1713) SS BOND : bond 0.00040 ( 2) SS BOND : angle 0.66325 ( 4) covalent geometry : bond 0.00267 (10084) covalent geometry : angle 0.53350 (13644) Misc. bond : bond 0.00136 ( 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 152 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 1.057 Fit side-chains REVERT: A 348 GLU cc_start: 0.7125 (mt-10) cc_final: 0.6739 (mt-10) REVERT: A 359 GLU cc_start: 0.6827 (mm-30) cc_final: 0.6068 (mt-10) REVERT: A 505 GLN cc_start: 0.8362 (OUTLIER) cc_final: 0.8070 (mt0) REVERT: A 590 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8471 (mt) REVERT: A 617 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.7891 (tt0) REVERT: A 682 ILE cc_start: 0.8535 (mt) cc_final: 0.8138 (mp) REVERT: B 359 GLU cc_start: 0.6885 (mm-30) cc_final: 0.6138 (mt-10) REVERT: B 362 LYS cc_start: 0.7117 (mttt) cc_final: 0.6862 (mttt) REVERT: B 398 ARG cc_start: 0.7529 (ttm-80) cc_final: 0.7193 (mmt-90) REVERT: B 505 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.8065 (mt0) REVERT: B 590 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8488 (mt) REVERT: B 617 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.7890 (tt0) outliers start: 21 outliers final: 8 residues processed: 144 average time/residue: 1.5280 time to fit residues: 233.5263 Evaluate side-chains 135 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 1.035 ------------------------------------------------------------------------------- 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 505 GLN Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 617 GLN Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 505 GLN Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 617 GLN Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 651 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 76 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 38 optimal weight: 0.4980 chunk 64 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 108 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 22 optimal weight: 0.4980 chunk 16 optimal weight: 0.0070 chunk 1 optimal weight: 5.9990 chunk 105 optimal weight: 6.9990 overall best weight: 2.4002 ------------------------------------------------------------------------------- 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 140 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.142630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.102326 restraints weight = 8754.070| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 1.48 r_work: 0.2970 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 10088 Z= 0.230 Angle : 0.641 8.410 13648 Z= 0.324 Chirality : 0.047 0.194 1574 Planarity : 0.005 0.051 1692 Dihedral : 7.450 127.303 1372 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.42 % Allowed : 10.89 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.23), residues: 1232 helix: 1.26 (0.18), residues: 746 sheet: -0.02 (0.48), residues: 86 loop : -0.80 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 429 HIS 0.006 0.002 HIS B 248 PHE 0.026 0.002 PHE A 608 TYR 0.035 0.003 TYR A 592 ARG 0.004 0.001 ARG A 239 Details of bonding type rmsd hydrogen bonds : bond 0.05153 ( 575) hydrogen bonds : angle 4.08134 ( 1713) SS BOND : bond 0.00048 ( 2) SS BOND : angle 0.91396 ( 4) covalent geometry : bond 0.00540 (10084) covalent geometry : angle 0.64115 (13644) Misc. bond : bond 0.00187 ( 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 153 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 1.070 Fit side-chains REVERT: A 348 GLU cc_start: 0.7151 (mt-10) cc_final: 0.6753 (mt-10) REVERT: A 359 GLU cc_start: 0.6838 (mm-30) cc_final: 0.6030 (mt-10) REVERT: A 505 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.8118 (mt0) REVERT: A 682 ILE cc_start: 0.8554 (mt) cc_final: 0.8167 (mp) REVERT: B 359 GLU cc_start: 0.6890 (mm-30) cc_final: 0.6095 (mt-10) REVERT: B 362 LYS cc_start: 0.7123 (mttt) cc_final: 0.6848 (mttt) REVERT: B 505 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.8116 (mt0) outliers start: 26 outliers final: 14 residues processed: 142 average time/residue: 1.5212 time to fit residues: 229.0499 Evaluate side-chains 137 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 THR 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 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 392 ILE Chi-restraints excluded: chain B residue 505 GLN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 90 optimal weight: 9.9990 chunk 123 optimal weight: 0.3980 chunk 111 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 50 optimal weight: 0.0040 chunk 56 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 overall best weight: 0.5994 ------------------------------------------------------------------------------- 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 = 0.3628 r_free = 0.3628 target = 0.146896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.107324 restraints weight = 8801.104| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 1.47 r_work: 0.3037 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 10088 Z= 0.103 Angle : 0.506 6.658 13648 Z= 0.252 Chirality : 0.040 0.145 1574 Planarity : 0.004 0.032 1692 Dihedral : 6.919 125.143 1372 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.77 % Allowed : 11.92 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.24), residues: 1232 helix: 1.79 (0.19), residues: 744 sheet: 0.01 (0.47), residues: 86 loop : -0.69 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 572 HIS 0.003 0.001 HIS B 248 PHE 0.017 0.001 PHE B 608 TYR 0.024 0.002 TYR A 592 ARG 0.002 0.000 ARG A 239 Details of bonding type rmsd hydrogen bonds : bond 0.03604 ( 575) hydrogen bonds : angle 3.70186 ( 1713) SS BOND : bond 0.00194 ( 2) SS BOND : angle 0.48162 ( 4) covalent geometry : bond 0.00220 (10084) covalent geometry : angle 0.50651 (13644) Misc. bond : bond 0.00153 ( 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 154 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 135 time to evaluate : 1.032 Fit side-chains REVERT: A 348 GLU cc_start: 0.7196 (mt-10) cc_final: 0.6819 (mt-10) REVERT: A 359 GLU cc_start: 0.6840 (mm-30) cc_final: 0.6016 (mt-10) REVERT: A 505 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.8069 (mt0) REVERT: A 617 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.7870 (tt0) REVERT: A 682 ILE cc_start: 0.8533 (mt) cc_final: 0.8143 (mp) REVERT: B 348 GLU cc_start: 0.7267 (mt-10) cc_final: 0.6969 (mt-10) REVERT: B 359 GLU cc_start: 0.6857 (mm-30) cc_final: 0.6049 (mt-10) REVERT: B 362 LYS cc_start: 0.7045 (mttt) cc_final: 0.6732 (mttt) REVERT: B 505 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.8056 (mt0) REVERT: B 617 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.7872 (tt0) outliers start: 19 outliers final: 9 residues processed: 147 average time/residue: 1.3828 time to fit residues: 216.5139 Evaluate side-chains 139 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 1.016 ------------------------------------------------------------------------------- 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 541 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 617 GLN Chi-restraints excluded: chain A residue 628 VAL 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 617 GLN Chi-restraints excluded: chain B residue 628 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 34 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 88 optimal weight: 9.9990 chunk 64 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- 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 = 0.3577 r_free = 0.3577 target = 0.142407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.102117 restraints weight = 8826.340| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 1.50 r_work: 0.2965 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 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 : 0.005 0.035 10088 Z= 0.231 Angle : 0.635 8.368 13648 Z= 0.321 Chirality : 0.047 0.201 1574 Planarity : 0.005 0.047 1692 Dihedral : 7.382 126.949 1372 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.05 % Allowed : 12.38 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.23), residues: 1232 helix: 1.60 (0.18), residues: 746 sheet: -0.03 (0.47), residues: 86 loop : -0.65 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 364 HIS 0.005 0.002 HIS B 248 PHE 0.026 0.002 PHE B 608 TYR 0.040 0.003 TYR A 592 ARG 0.004 0.001 ARG B 239 Details of bonding type rmsd hydrogen bonds : bond 0.05005 ( 575) hydrogen bonds : angle 3.97139 ( 1713) SS BOND : bond 0.00064 ( 2) SS BOND : angle 0.74006 ( 4) covalent geometry : bond 0.00545 (10084) covalent geometry : angle 0.63479 (13644) Misc. bond : bond 0.00200 ( 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 155 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 1.108 Fit side-chains REVERT: A 359 GLU cc_start: 0.6830 (mm-30) cc_final: 0.5966 (mt-10) REVERT: A 505 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.8071 (mt0) REVERT: A 682 ILE cc_start: 0.8508 (mt) cc_final: 0.8115 (mp) REVERT: B 359 GLU cc_start: 0.6882 (mm-30) cc_final: 0.6047 (mt-10) REVERT: B 362 LYS cc_start: 0.7123 (mttt) cc_final: 0.5373 (mmtm) REVERT: B 505 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.8095 (mt0) outliers start: 22 outliers final: 17 residues processed: 145 average time/residue: 1.6126 time to fit residues: 247.0778 Evaluate side-chains 148 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 0.991 ------------------------------------------------------------------------------- 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 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 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 345 ARG 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 33 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 27 optimal weight: 10.0000 chunk 72 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 101 optimal weight: 0.0980 chunk 71 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3613 r_free = 0.3613 target = 0.145589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.106495 restraints weight = 8956.737| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.44 r_work: 0.3025 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 10088 Z= 0.115 Angle : 0.521 6.941 13648 Z= 0.260 Chirality : 0.040 0.145 1574 Planarity : 0.004 0.033 1692 Dihedral : 6.999 126.007 1372 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.58 % Allowed : 13.13 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.24), residues: 1232 helix: 1.97 (0.19), residues: 744 sheet: 0.08 (0.47), residues: 86 loop : -0.59 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 572 HIS 0.003 0.001 HIS B 248 PHE 0.017 0.001 PHE A 608 TYR 0.030 0.002 TYR A 592 ARG 0.002 0.000 ARG B 437 Details of bonding type rmsd hydrogen bonds : bond 0.03777 ( 575) hydrogen bonds : angle 3.69551 ( 1713) SS BOND : bond 0.00054 ( 2) SS BOND : angle 0.46352 ( 4) covalent geometry : bond 0.00253 (10084) covalent geometry : angle 0.52138 (13644) Misc. bond : bond 0.00127 ( 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 154 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 137 time to evaluate : 1.045 Fit side-chains REVERT: A 348 GLU cc_start: 0.7271 (mt-10) cc_final: 0.6985 (mt-10) REVERT: A 359 GLU cc_start: 0.6950 (mm-30) cc_final: 0.6132 (mt-10) REVERT: A 505 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.8097 (mt0) REVERT: A 609 PHE cc_start: 0.7802 (OUTLIER) cc_final: 0.7335 (t80) REVERT: A 682 ILE cc_start: 0.8591 (mt) cc_final: 0.8217 (mp) REVERT: B 359 GLU cc_start: 0.6947 (mm-30) cc_final: 0.6125 (mt-10) REVERT: B 362 LYS cc_start: 0.7258 (mttt) cc_final: 0.7026 (mtpt) REVERT: B 505 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.8081 (mt0) REVERT: B 609 PHE cc_start: 0.7799 (OUTLIER) cc_final: 0.7330 (t80) outliers start: 17 outliers final: 9 residues processed: 145 average time/residue: 1.5042 time to fit residues: 231.2951 Evaluate side-chains 141 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 128 time to evaluate : 1.102 ------------------------------------------------------------------------------- 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 392 ILE Chi-restraints excluded: chain A residue 505 GLN Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 609 PHE Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain B residue 104 THR 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 609 PHE Chi-restraints excluded: chain B residue 628 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 36 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 56 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 108 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 442 ASN ** A 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3559 r_free = 0.3559 target = 0.140943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.101072 restraints weight = 8920.796| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.47 r_work: 0.2958 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 10088 Z= 0.260 Angle : 0.667 8.588 13648 Z= 0.337 Chirality : 0.049 0.197 1574 Planarity : 0.005 0.059 1692 Dihedral : 7.456 127.162 1372 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.51 % Allowed : 12.76 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.23), residues: 1232 helix: 1.57 (0.18), residues: 746 sheet: 0.02 (0.47), residues: 86 loop : -0.62 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 364 HIS 0.005 0.002 HIS B 248 PHE 0.027 0.003 PHE A 608 TYR 0.048 0.003 TYR A 592 ARG 0.006 0.001 ARG A 239 Details of bonding type rmsd hydrogen bonds : bond 0.05244 ( 575) hydrogen bonds : angle 4.00619 ( 1713) SS BOND : bond 0.00106 ( 2) SS BOND : angle 0.79454 ( 4) covalent geometry : bond 0.00616 (10084) covalent geometry : angle 0.66651 (13644) Misc. bond : bond 0.00188 ( 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 158 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 131 time to evaluate : 1.032 Fit side-chains REVERT: A 359 GLU cc_start: 0.6850 (mm-30) cc_final: 0.5991 (mt-10) REVERT: A 505 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.8109 (mt0) REVERT: A 609 PHE cc_start: 0.7872 (OUTLIER) cc_final: 0.7398 (t80) REVERT: A 682 ILE cc_start: 0.8523 (mt) cc_final: 0.8144 (mp) REVERT: B 359 GLU cc_start: 0.6893 (mm-30) cc_final: 0.6032 (mt-10) REVERT: B 362 LYS cc_start: 0.7159 (mttt) cc_final: 0.5404 (mmtm) REVERT: B 505 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.8102 (mt0) REVERT: B 609 PHE cc_start: 0.7872 (OUTLIER) cc_final: 0.7398 (t80) outliers start: 27 outliers final: 14 residues processed: 146 average time/residue: 1.5697 time to fit residues: 242.3415 Evaluate side-chains 148 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 1.023 ------------------------------------------------------------------------------- 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 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 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 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 609 PHE Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 651 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 57 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 chunk 102 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3584 r_free = 0.3584 target = 0.143105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.103530 restraints weight = 8903.667| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 1.47 r_work: 0.2991 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10088 Z= 0.159 Angle : 0.574 7.699 13648 Z= 0.287 Chirality : 0.043 0.157 1574 Planarity : 0.004 0.034 1692 Dihedral : 7.207 126.268 1372 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.86 % Allowed : 13.31 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.24), residues: 1232 helix: 1.77 (0.19), residues: 744 sheet: 0.07 (0.47), residues: 86 loop : -0.59 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 572 HIS 0.004 0.001 HIS A 248 PHE 0.021 0.002 PHE B 608 TYR 0.042 0.002 TYR A 592 ARG 0.002 0.000 ARG B 294 Details of bonding type rmsd hydrogen bonds : bond 0.04317 ( 575) hydrogen bonds : angle 3.82575 ( 1713) SS BOND : bond 0.00011 ( 2) SS BOND : angle 0.53935 ( 4) covalent geometry : bond 0.00368 (10084) covalent geometry : angle 0.57360 (13644) Misc. bond : bond 0.00178 ( 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 149 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 1.391 Fit side-chains REVERT: A 359 GLU cc_start: 0.6896 (mm-30) cc_final: 0.6079 (mt-10) REVERT: A 505 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.8085 (mt0) REVERT: A 609 PHE cc_start: 0.7768 (OUTLIER) cc_final: 0.7315 (t80) REVERT: A 682 ILE cc_start: 0.8484 (mt) cc_final: 0.8081 (mp) REVERT: B 348 GLU cc_start: 0.7335 (mt-10) cc_final: 0.7099 (mt-10) REVERT: B 359 GLU cc_start: 0.6901 (mm-30) cc_final: 0.6064 (mt-10) REVERT: B 362 LYS cc_start: 0.7209 (mttt) cc_final: 0.6976 (mtpt) REVERT: B 505 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.8079 (mt0) REVERT: B 609 PHE cc_start: 0.7768 (OUTLIER) cc_final: 0.7312 (t80) outliers start: 20 outliers final: 13 residues processed: 142 average time/residue: 1.5046 time to fit residues: 226.3138 Evaluate side-chains 143 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 1.047 ------------------------------------------------------------------------------- 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 609 PHE 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 505 GLN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 86 optimal weight: 10.0000 chunk 114 optimal weight: 0.5980 chunk 55 optimal weight: 0.6980 chunk 69 optimal weight: 0.0030 chunk 118 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 78 optimal weight: 0.4980 chunk 45 optimal weight: 1.9990 chunk 24 optimal weight: 9.9990 chunk 117 optimal weight: 7.9990 chunk 57 optimal weight: 10.0000 overall best weight: 0.5590 ------------------------------------------------------------------------------- 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 = 0.3628 r_free = 0.3628 target = 0.146888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.107505 restraints weight = 8899.135| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 1.49 r_work: 0.3042 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2100 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= 0.103 Angle : 0.507 6.518 13648 Z= 0.252 Chirality : 0.040 0.146 1574 Planarity : 0.004 0.034 1692 Dihedral : 6.794 122.825 1372 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.30 % Allowed : 13.87 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.24), residues: 1232 helix: 2.14 (0.19), residues: 744 sheet: 0.18 (0.46), residues: 86 loop : -0.56 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 572 HIS 0.002 0.001 HIS B 248 PHE 0.017 0.001 PHE B 608 TYR 0.034 0.002 TYR A 592 ARG 0.003 0.000 ARG B 239 Details of bonding type rmsd hydrogen bonds : bond 0.03562 ( 575) hydrogen bonds : angle 3.61440 ( 1713) SS BOND : bond 0.00035 ( 2) SS BOND : angle 0.49705 ( 4) covalent geometry : bond 0.00224 (10084) covalent geometry : angle 0.50724 (13644) Misc. bond : bond 0.00116 ( 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 148 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 134 time to evaluate : 1.145 Fit side-chains REVERT: A 359 GLU cc_start: 0.6855 (mm-30) cc_final: 0.6052 (mt-10) REVERT: A 505 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.8097 (mt0) REVERT: B 359 GLU cc_start: 0.6860 (mm-30) cc_final: 0.6010 (mt-10) REVERT: B 362 LYS cc_start: 0.7149 (mttt) cc_final: 0.6901 (mtpt) REVERT: B 505 GLN cc_start: 0.8313 (OUTLIER) cc_final: 0.8069 (mt0) outliers start: 14 outliers final: 8 residues processed: 145 average time/residue: 1.4757 time to fit residues: 227.2717 Evaluate side-chains 143 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 133 time to evaluate : 1.154 ------------------------------------------------------------------------------- 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 628 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 76 optimal weight: 0.0980 chunk 13 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 119 optimal weight: 10.0000 chunk 94 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 95 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.3586 r_free = 0.3586 target = 0.143205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.103957 restraints weight = 8890.861| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 1.43 r_work: 0.2992 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10088 Z= 0.169 Angle : 0.584 7.957 13648 Z= 0.292 Chirality : 0.044 0.171 1574 Planarity : 0.004 0.035 1692 Dihedral : 7.207 126.924 1372 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.40 % Allowed : 14.80 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.24), residues: 1232 helix: 1.88 (0.19), residues: 748 sheet: 0.15 (0.46), residues: 86 loop : -0.60 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 572 HIS 0.004 0.001 HIS B 248 PHE 0.021 0.002 PHE B 608 TYR 0.049 0.003 TYR A 592 ARG 0.004 0.000 ARG A 161 Details of bonding type rmsd hydrogen bonds : bond 0.04416 ( 575) hydrogen bonds : angle 3.79275 ( 1713) SS BOND : bond 0.00014 ( 2) SS BOND : angle 0.56421 ( 4) covalent geometry : bond 0.00395 (10084) covalent geometry : angle 0.58397 (13644) Misc. bond : bond 0.00199 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8169.81 seconds wall clock time: 140 minutes 56.25 seconds (8456.25 seconds total)