Starting phenix.real_space_refine on Sun Dec 29 05:28:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wto_37838/12_2024/8wto_37838.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wto_37838/12_2024/8wto_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_37838/12_2024/8wto_37838.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wto_37838/12_2024/8wto_37838.map" model { file = "/net/cci-nas-00/data/ceres_data/8wto_37838/12_2024/8wto_37838.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wto_37838/12_2024/8wto_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 6.47, per 1000 atoms: 0.65 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: 2.75 Conformation dependent library (CDL) restraints added in 1.2 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: 1.21 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: 3.42 Time building geometry restraints manager: 3.08 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: 0.00 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: 0.010 Normalize map: mean=0, sd=1: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 26.490 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 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:13.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.420 ------------------------------------------------------------------------------- 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 : 0.010 0.281 10084 Z= 0.583 Angle : 1.042 25.339 13644 Z= 0.507 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 *********************** 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 : 1.244 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: 1.6930 time to fit residues: 319.9502 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 : 1.173 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 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 10084 Z= 0.224 Angle : 0.595 7.134 13644 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 *********************** 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 : 1.171 Fit side-chains REVERT: A 272 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8313 (mtmm) REVERT: A 359 GLU cc_start: 0.7109 (mm-30) cc_final: 0.6703 (mt-10) REVERT: A 666 MET cc_start: 0.7827 (tpp) cc_final: 0.7606 (tpp) REVERT: A 682 ILE cc_start: 0.8901 (mt) cc_final: 0.8528 (mp) REVERT: A 697 GLN cc_start: 0.8500 (mt0) cc_final: 0.8289 (mt0) REVERT: B 272 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8311 (mtmm) REVERT: B 359 GLU cc_start: 0.7084 (mm-30) cc_final: 0.6663 (mt-10) REVERT: B 362 LYS cc_start: 0.7957 (mttt) cc_final: 0.7733 (mttt) REVERT: B 682 ILE cc_start: 0.8868 (mt) cc_final: 0.8471 (mp) REVERT: B 697 GLN cc_start: 0.8497 (mt0) cc_final: 0.8287 (mt0) outliers start: 20 outliers final: 13 residues processed: 144 average time/residue: 1.6239 time to fit residues: 247.6608 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 : 1.243 ------------------------------------------------------------------------------- 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 62 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 76 optimal weight: 0.1980 chunk 31 optimal weight: 0.6980 chunk 112 optimal weight: 1.9990 chunk 121 optimal weight: 0.7980 chunk 100 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 90 optimal weight: 8.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10084 Z= 0.177 Angle : 0.540 7.197 13644 Z= 0.271 Chirality : 0.041 0.145 1574 Planarity : 0.004 0.034 1692 Dihedral : 7.149 126.830 1372 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 4.30 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: 0.57 (0.23), residues: 1232 helix: 1.13 (0.18), residues: 744 sheet: 0.02 (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 B 608 TYR 0.025 0.002 TYR A 592 ARG 0.003 0.000 ARG A 161 *********************** 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 150 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 1.342 Fit side-chains REVERT: A 272 LYS cc_start: 0.8625 (OUTLIER) cc_final: 0.8323 (mtmm) REVERT: A 359 GLU cc_start: 0.7127 (mm-30) cc_final: 0.6696 (mt-10) REVERT: A 505 GLN cc_start: 0.7926 (OUTLIER) cc_final: 0.7618 (mt0) REVERT: A 617 GLN cc_start: 0.7391 (OUTLIER) cc_final: 0.7002 (tt0) REVERT: A 620 ILE cc_start: 0.8671 (mm) cc_final: 0.8468 (mm) REVERT: A 682 ILE cc_start: 0.8902 (mt) cc_final: 0.8515 (mp) REVERT: B 272 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8315 (mtmm) REVERT: B 359 GLU cc_start: 0.7116 (mm-30) cc_final: 0.6681 (mt-10) REVERT: B 362 LYS cc_start: 0.7979 (mttt) cc_final: 0.7735 (mttt) REVERT: B 505 GLN cc_start: 0.7920 (OUTLIER) cc_final: 0.7617 (mt0) REVERT: B 617 GLN cc_start: 0.7393 (OUTLIER) cc_final: 0.6999 (tt0) REVERT: B 620 ILE cc_start: 0.8672 (mm) cc_final: 0.8468 (mm) outliers start: 21 outliers final: 7 residues processed: 142 average time/residue: 1.6312 time to fit residues: 245.3241 Evaluate side-chains 134 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 1.203 ------------------------------------------------------------------------------- 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 505 GLN 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 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 505 GLN 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 111 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 75 optimal weight: 5.9990 chunk 113 optimal weight: 0.9980 chunk 119 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 10084 Z= 0.394 Angle : 0.673 8.506 13644 Z= 0.342 Chirality : 0.049 0.207 1574 Planarity : 0.005 0.062 1692 Dihedral : 7.529 127.318 1372 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.61 % Allowed : 10.99 % Favored : 86.41 % 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 (0.23), residues: 1232 helix: 1.19 (0.18), residues: 746 sheet: -0.00 (0.49), residues: 86 loop : -0.80 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 621 HIS 0.006 0.002 HIS B 248 PHE 0.028 0.003 PHE B 608 TYR 0.036 0.003 TYR A 592 ARG 0.006 0.001 ARG A 239 *********************** 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 159 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 131 time to evaluate : 1.208 Fit side-chains REVERT: A 359 GLU cc_start: 0.7119 (mm-30) cc_final: 0.6657 (mt-10) REVERT: A 505 GLN cc_start: 0.7955 (OUTLIER) cc_final: 0.7682 (mt0) REVERT: A 620 ILE cc_start: 0.8767 (mm) cc_final: 0.8556 (mm) REVERT: A 682 ILE cc_start: 0.8895 (mt) cc_final: 0.8528 (mp) REVERT: B 359 GLU cc_start: 0.7100 (mm-30) cc_final: 0.6597 (mt-10) REVERT: B 362 LYS cc_start: 0.7933 (mttt) cc_final: 0.7682 (mttt) REVERT: B 505 GLN cc_start: 0.7951 (OUTLIER) cc_final: 0.7678 (mt0) REVERT: B 620 ILE cc_start: 0.8763 (mm) cc_final: 0.8551 (mm) outliers start: 28 outliers final: 13 residues processed: 145 average time/residue: 1.6466 time to fit residues: 253.2261 Evaluate side-chains 144 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 1.200 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 102 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 61 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 30 optimal weight: 7.9990 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 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10084 Z= 0.281 Angle : 0.601 7.998 13644 Z= 0.303 Chirality : 0.045 0.172 1574 Planarity : 0.004 0.036 1692 Dihedral : 7.342 126.420 1372 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.42 % Allowed : 11.45 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.23), residues: 1232 helix: 1.47 (0.18), residues: 746 sheet: -0.05 (0.48), residues: 86 loop : -0.73 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 364 HIS 0.005 0.001 HIS B 248 PHE 0.024 0.002 PHE B 608 TYR 0.031 0.002 TYR A 592 ARG 0.004 0.001 ARG B 294 *********************** 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 164 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 1.187 Fit side-chains REVERT: A 272 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8281 (mtmm) REVERT: A 359 GLU cc_start: 0.7118 (mm-30) cc_final: 0.6632 (mt-10) REVERT: A 505 GLN cc_start: 0.7937 (OUTLIER) cc_final: 0.7659 (mt0) REVERT: A 620 ILE cc_start: 0.8707 (mm) cc_final: 0.8487 (mm) REVERT: A 682 ILE cc_start: 0.8890 (mt) cc_final: 0.8524 (mp) REVERT: B 272 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8269 (mtmm) REVERT: B 359 GLU cc_start: 0.7133 (mm-30) cc_final: 0.6650 (mt-10) REVERT: B 362 LYS cc_start: 0.7968 (mttt) cc_final: 0.7668 (mttt) REVERT: B 505 GLN cc_start: 0.7931 (OUTLIER) cc_final: 0.7652 (mt0) REVERT: B 620 ILE cc_start: 0.8706 (mm) cc_final: 0.8484 (mm) outliers start: 26 outliers final: 15 residues processed: 150 average time/residue: 1.6640 time to fit residues: 263.8876 Evaluate side-chains 150 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 1.129 ------------------------------------------------------------------------------- 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 119 optimal weight: 9.9990 chunk 99 optimal weight: 4.9990 chunk 55 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 10084 Z= 0.247 Angle : 0.581 7.811 13644 Z= 0.292 Chirality : 0.043 0.168 1574 Planarity : 0.004 0.031 1692 Dihedral : 7.272 126.611 1372 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.33 % Allowed : 12.38 % 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: 1.16 (0.23), residues: 1232 helix: 1.66 (0.18), residues: 744 sheet: -0.01 (0.48), residues: 86 loop : -0.69 (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 B 248 PHE 0.022 0.002 PHE B 608 TYR 0.035 0.002 TYR A 592 ARG 0.004 0.000 ARG A 161 *********************** 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 162 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 137 time to evaluate : 1.139 Fit side-chains REVERT: A 272 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8285 (mtmm) REVERT: A 359 GLU cc_start: 0.7113 (mm-30) cc_final: 0.6618 (mt-10) REVERT: A 505 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.7639 (mt0) REVERT: A 620 ILE cc_start: 0.8697 (mm) cc_final: 0.8485 (mm) REVERT: A 682 ILE cc_start: 0.8889 (mt) cc_final: 0.8530 (mp) REVERT: B 272 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.8279 (mtmm) REVERT: B 359 GLU cc_start: 0.7135 (mm-30) cc_final: 0.6624 (mt-10) REVERT: B 362 LYS cc_start: 0.7964 (mttt) cc_final: 0.6310 (mmtm) REVERT: B 505 GLN cc_start: 0.7920 (OUTLIER) cc_final: 0.7642 (mt0) REVERT: B 620 ILE cc_start: 0.8698 (mm) cc_final: 0.8484 (mm) outliers start: 25 outliers final: 14 residues processed: 153 average time/residue: 1.6939 time to fit residues: 273.7912 Evaluate side-chains 152 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 1.435 ------------------------------------------------------------------------------- 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 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 272 LYS 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 87 optimal weight: 9.9990 chunk 67 optimal weight: 0.1980 chunk 100 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 119 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 chunk 72 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 442 ASN ** B 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10084 Z= 0.250 Angle : 0.582 7.838 13644 Z= 0.292 Chirality : 0.044 0.168 1574 Planarity : 0.004 0.033 1692 Dihedral : 7.263 126.772 1372 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.79 % Allowed : 12.20 % Favored : 85.01 % 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: 1.23 (0.23), residues: 1232 helix: 1.71 (0.18), residues: 744 sheet: -0.01 (0.47), residues: 86 loop : -0.65 (0.31), residues: 402 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 0.022 0.002 PHE B 608 TYR 0.038 0.002 TYR A 592 ARG 0.004 0.000 ARG A 161 *********************** 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: 30 poor density : 135 time to evaluate : 1.189 Fit side-chains REVERT: A 272 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8282 (mtmm) REVERT: A 359 GLU cc_start: 0.7157 (mm-30) cc_final: 0.6670 (mt-10) REVERT: A 505 GLN cc_start: 0.7917 (OUTLIER) cc_final: 0.7637 (mt0) REVERT: A 511 MET cc_start: 0.8376 (mtt) cc_final: 0.8143 (mtt) REVERT: A 609 PHE cc_start: 0.7670 (OUTLIER) cc_final: 0.7293 (t80) REVERT: A 620 ILE cc_start: 0.8703 (mm) cc_final: 0.8493 (mm) REVERT: A 666 MET cc_start: 0.7862 (tpp) cc_final: 0.7654 (tpt) REVERT: A 682 ILE cc_start: 0.8894 (mt) cc_final: 0.8543 (mp) REVERT: B 272 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8271 (mtmm) REVERT: B 359 GLU cc_start: 0.7137 (mm-30) cc_final: 0.6621 (mt-10) REVERT: B 362 LYS cc_start: 0.7977 (mttt) cc_final: 0.6329 (mmtm) REVERT: B 505 GLN cc_start: 0.7909 (OUTLIER) cc_final: 0.7629 (mt0) REVERT: B 511 MET cc_start: 0.8381 (mtt) cc_final: 0.8144 (mtt) REVERT: B 609 PHE cc_start: 0.7670 (OUTLIER) cc_final: 0.7292 (t80) REVERT: B 620 ILE cc_start: 0.8697 (mm) cc_final: 0.8483 (mm) outliers start: 30 outliers final: 20 residues processed: 153 average time/residue: 1.5986 time to fit residues: 259.2435 Evaluate side-chains 156 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 1.200 ------------------------------------------------------------------------------- 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 345 ARG 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 557 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 73 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10084 Z= 0.231 Angle : 0.568 7.702 13644 Z= 0.285 Chirality : 0.043 0.161 1574 Planarity : 0.004 0.033 1692 Dihedral : 7.216 126.649 1372 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.51 % Allowed : 12.85 % 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 (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: 1.32 (0.23), residues: 1232 helix: 1.78 (0.18), residues: 744 sheet: 0.02 (0.47), residues: 86 loop : -0.62 (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 B 248 PHE 0.021 0.002 PHE B 608 TYR 0.040 0.002 TYR A 592 ARG 0.004 0.000 ARG A 161 *********************** 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 163 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 136 time to evaluate : 1.246 Fit side-chains REVERT: A 272 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8296 (mtmm) REVERT: A 359 GLU cc_start: 0.7152 (mm-30) cc_final: 0.6662 (mt-10) REVERT: A 505 GLN cc_start: 0.7920 (OUTLIER) cc_final: 0.7625 (mt0) REVERT: A 511 MET cc_start: 0.8387 (mtt) cc_final: 0.8162 (mtt) REVERT: A 609 PHE cc_start: 0.7668 (OUTLIER) cc_final: 0.7292 (t80) REVERT: A 620 ILE cc_start: 0.8702 (mm) cc_final: 0.8499 (mm) REVERT: A 682 ILE cc_start: 0.8883 (mt) cc_final: 0.8501 (mp) REVERT: B 272 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8266 (mtmm) REVERT: B 359 GLU cc_start: 0.7137 (mm-30) cc_final: 0.6627 (mt-10) REVERT: B 362 LYS cc_start: 0.7975 (mttt) cc_final: 0.6344 (mmtm) REVERT: B 505 GLN cc_start: 0.7911 (OUTLIER) cc_final: 0.7632 (mt0) REVERT: B 511 MET cc_start: 0.8392 (mtt) cc_final: 0.8161 (mtt) REVERT: B 609 PHE cc_start: 0.7668 (OUTLIER) cc_final: 0.7290 (t80) REVERT: B 620 ILE cc_start: 0.8701 (mm) cc_final: 0.8497 (mm) outliers start: 27 outliers final: 19 residues processed: 153 average time/residue: 1.5355 time to fit residues: 249.4263 Evaluate side-chains 149 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 1.206 ------------------------------------------------------------------------------- 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 557 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 67 optimal weight: 0.3980 chunk 48 optimal weight: 2.9990 chunk 87 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 105 optimal weight: 0.8980 chunk 110 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10084 Z= 0.167 Angle : 0.526 6.988 13644 Z= 0.262 Chirality : 0.041 0.150 1574 Planarity : 0.004 0.033 1692 Dihedral : 6.995 125.631 1372 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.14 % Allowed : 13.31 % 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 (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: 1.50 (0.24), residues: 1232 helix: 1.95 (0.19), residues: 748 sheet: 0.09 (0.47), residues: 86 loop : -0.63 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 572 HIS 0.003 0.001 HIS B 248 PHE 0.018 0.001 PHE B 608 TYR 0.037 0.002 TYR A 592 ARG 0.004 0.000 ARG A 161 *********************** 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 158 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 1.308 Fit side-chains REVERT: A 359 GLU cc_start: 0.7145 (mm-30) cc_final: 0.6676 (mt-10) REVERT: A 505 GLN cc_start: 0.7903 (OUTLIER) cc_final: 0.7625 (mt0) REVERT: A 511 MET cc_start: 0.8376 (mtt) cc_final: 0.8143 (mtt) REVERT: A 609 PHE cc_start: 0.7589 (OUTLIER) cc_final: 0.7229 (t80) REVERT: A 682 ILE cc_start: 0.8880 (mt) cc_final: 0.8499 (mp) REVERT: B 272 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8289 (mtmm) REVERT: B 359 GLU cc_start: 0.7124 (mm-30) cc_final: 0.6617 (mt-10) REVERT: B 362 LYS cc_start: 0.7973 (mttt) cc_final: 0.7733 (mtpt) REVERT: B 505 GLN cc_start: 0.7892 (OUTLIER) cc_final: 0.7610 (mt0) REVERT: B 511 MET cc_start: 0.8374 (mtt) cc_final: 0.8139 (mtt) REVERT: B 609 PHE cc_start: 0.7592 (OUTLIER) cc_final: 0.7229 (t80) outliers start: 23 outliers final: 13 residues processed: 149 average time/residue: 1.5180 time to fit residues: 240.5264 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 : 1.233 ------------------------------------------------------------------------------- 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 590 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 272 LYS 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 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 117 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 81 optimal weight: 5.9990 chunk 123 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 98 optimal weight: 0.0980 chunk 10 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10084 Z= 0.281 Angle : 0.601 8.136 13644 Z= 0.302 Chirality : 0.045 0.177 1574 Planarity : 0.004 0.035 1692 Dihedral : 7.290 127.158 1372 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.14 % Allowed : 13.41 % Favored : 84.45 % 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 (0.23), residues: 1232 helix: 1.77 (0.18), residues: 746 sheet: 0.08 (0.47), residues: 86 loop : -0.60 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 364 HIS 0.004 0.001 HIS B 248 PHE 0.023 0.002 PHE B 608 TYR 0.051 0.003 TYR A 592 ARG 0.004 0.000 ARG A 161 ********************** 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 146 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 1.199 Fit side-chains REVERT: A 359 GLU cc_start: 0.7185 (mm-30) cc_final: 0.6678 (mt-10) REVERT: A 505 GLN cc_start: 0.7951 (OUTLIER) cc_final: 0.7655 (mt0) REVERT: A 609 PHE cc_start: 0.7675 (OUTLIER) cc_final: 0.7294 (t80) REVERT: A 682 ILE cc_start: 0.8883 (mt) cc_final: 0.8504 (mp) REVERT: B 272 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8279 (mtmm) REVERT: B 359 GLU cc_start: 0.7168 (mm-30) cc_final: 0.6648 (mt-10) REVERT: B 362 LYS cc_start: 0.7978 (mttt) cc_final: 0.6338 (mmtm) REVERT: B 505 GLN cc_start: 0.7944 (OUTLIER) cc_final: 0.7645 (mt0) REVERT: B 609 PHE cc_start: 0.7677 (OUTLIER) cc_final: 0.7295 (t80) outliers start: 23 outliers final: 16 residues processed: 137 average time/residue: 1.6249 time to fit residues: 235.6089 Evaluate side-chains 142 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 1.165 ------------------------------------------------------------------------------- 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 590 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 272 LYS 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 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 104 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 90 optimal weight: 7.9990 chunk 14 optimal weight: 0.0040 chunk 27 optimal weight: 10.0000 chunk 98 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 86 optimal weight: 10.0000 overall best weight: 1.5796 ------------------------------------------------------------------------------- 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 = 0.3584 r_free = 0.3584 target = 0.143073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.104032 restraints weight = 8904.501| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 1.43 r_work: 0.2985 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10084 Z= 0.253 Angle : 0.583 7.786 13644 Z= 0.293 Chirality : 0.044 0.171 1574 Planarity : 0.004 0.034 1692 Dihedral : 7.236 127.254 1372 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.05 % Allowed : 13.41 % 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 (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: 1.35 (0.23), residues: 1232 helix: 1.80 (0.18), residues: 744 sheet: 0.06 (0.47), residues: 86 loop : -0.58 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 364 HIS 0.004 0.001 HIS B 248 PHE 0.022 0.002 PHE B 608 TYR 0.052 0.003 TYR A 592 ARG 0.004 0.000 ARG A 161 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4228.44 seconds wall clock time: 76 minutes 14.30 seconds (4574.30 seconds total)