Starting phenix.real_space_refine on Wed Feb 4 23:50:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uep_64088/02_2026/9uep_64088.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uep_64088/02_2026/9uep_64088.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9uep_64088/02_2026/9uep_64088.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uep_64088/02_2026/9uep_64088.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9uep_64088/02_2026/9uep_64088.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uep_64088/02_2026/9uep_64088.map" } resolution = 2.85 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.027 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 6382 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: 4 Type Number sf(0) Gaussians S 33 5.16 5 C 5449 2.51 5 N 1394 2.21 5 O 1638 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8514 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1146 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 141} Chain: "C" Number of atoms: 7207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 902, 7207 Classifications: {'peptide': 902} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 45, 'TRANS': 856} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 2, 'ARG:plan': 2, 'GLN:plan1': 2, 'GLU:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "B" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 1.87, per 1000 atoms: 0.22 Number of scatterers: 8514 At special positions: 0 Unit cell: (103.5, 129.03, 95.91, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 33 16.00 O 1638 8.00 N 1394 7.00 C 5449 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 552 " - pdb=" SG CYS A 611 " distance=2.03 Simple disulfide: pdb=" SG CYS C 770 " - pdb=" SG CYS C 777 " distance=2.03 Simple disulfide: pdb=" SG CYS C 807 " - pdb=" SG CYS C 843 " 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=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " BETA1-6 " NAG B 1 " - " FUC B 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A 701 " - " ASN A 538 " " NAG B 1 " - " ASN C 748 " " NAG C1001 " - " ASN C 92 " " NAG C1002 " - " ASN C 241 " " NAG C1003 " - " ASN C 134 " " NAG D 1 " - " ASN C 634 " " NAG E 1 " - " ASN C 690 " Time building additional restraints: 0.78 Conformation dependent library (CDL) restraints added in 214.4 milliseconds 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2004 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 13 sheets defined 44.8% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 580 through 584 removed outlier: 3.808A pdb=" N GLU A 584 " --> pdb=" O ASP A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 604 removed outlier: 3.550A pdb=" N ASN A 603 " --> pdb=" O ASP A 599 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR A 604 " --> pdb=" O LYS A 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 287 removed outlier: 3.519A pdb=" N LEU C 286 " --> pdb=" O SER C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 319 Processing helix chain 'C' and resid 321 through 340 removed outlier: 3.608A pdb=" N LEU C 325 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLY C 329 " --> pdb=" O LEU C 325 " (cutoff:3.500A) Proline residue: C 330 - end of helix Processing helix chain 'C' and resid 372 through 374 No H-bonds generated for 'chain 'C' and resid 372 through 374' Processing helix chain 'C' and resid 382 through 398 Processing helix chain 'C' and resid 410 through 412 No H-bonds generated for 'chain 'C' and resid 410 through 412' Processing helix chain 'C' and resid 413 through 433 removed outlier: 4.263A pdb=" N ASN C 417 " --> pdb=" O ASP C 413 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N TYR C 426 " --> pdb=" O SER C 422 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU C 427 " --> pdb=" O TYR C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 434 through 439 removed outlier: 3.990A pdb=" N ASN C 437 " --> pdb=" O PRO C 434 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU C 438 " --> pdb=" O THR C 435 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N LYS C 439 " --> pdb=" O TRP C 436 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 434 through 439' Processing helix chain 'C' and resid 440 through 446 removed outlier: 4.269A pdb=" N LEU C 444 " --> pdb=" O ASP C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 455 removed outlier: 3.645A pdb=" N VAL C 453 " --> pdb=" O ARG C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 478 removed outlier: 3.663A pdb=" N VAL C 478 " --> pdb=" O GLN C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 497 removed outlier: 4.578A pdb=" N GLY C 487 " --> pdb=" O SER C 483 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ALA C 488 " --> pdb=" O TYR C 484 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE C 497 " --> pdb=" O MET C 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 514 removed outlier: 3.975A pdb=" N LYS C 504 " --> pdb=" O GLU C 500 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N MET C 505 " --> pdb=" O ASP C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 535 removed outlier: 4.138A pdb=" N LEU C 524 " --> pdb=" O ILE C 520 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N TRP C 525 " --> pdb=" O TYR C 521 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS C 534 " --> pdb=" O GLN C 530 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLN C 535 " --> pdb=" O VAL C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 554 removed outlier: 4.053A pdb=" N ARG C 550 " --> pdb=" O ALA C 546 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N TRP C 551 " --> pdb=" O ILE C 547 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLN C 554 " --> pdb=" O ARG C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 619 through 622 Processing helix chain 'C' and resid 633 through 636 Processing helix chain 'C' and resid 644 through 658 Processing helix chain 'C' and resid 663 through 680 removed outlier: 3.781A pdb=" N ILE C 671 " --> pdb=" O ARG C 667 " (cutoff:3.500A) Processing helix chain 'C' and resid 684 through 691 removed outlier: 3.556A pdb=" N ALA C 688 " --> pdb=" O PRO C 684 " (cutoff:3.500A) Processing helix chain 'C' and resid 692 through 698 removed outlier: 3.856A pdb=" N ILE C 696 " --> pdb=" O LEU C 693 " (cutoff:3.500A) Processing helix chain 'C' and resid 700 through 719 removed outlier: 4.003A pdb=" N TRP C 704 " --> pdb=" O GLU C 700 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N TYR C 713 " --> pdb=" O SER C 709 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N PHE C 714 " --> pdb=" O SER C 710 " (cutoff:3.500A) Processing helix chain 'C' and resid 723 through 746 Proline residue: C 737 - end of helix Processing helix chain 'C' and resid 755 through 773 removed outlier: 3.635A pdb=" N ILE C 763 " --> pdb=" O GLN C 759 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN C 764 " --> pdb=" O TYR C 760 " (cutoff:3.500A) Processing helix chain 'C' and resid 774 through 790 removed outlier: 3.625A pdb=" N GLU C 778 " --> pdb=" O VAL C 774 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN C 787 " --> pdb=" O THR C 783 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS C 790 " --> pdb=" O ALA C 786 " (cutoff:3.500A) Processing helix chain 'C' and resid 798 through 800 No H-bonds generated for 'chain 'C' and resid 798 through 800' Processing helix chain 'C' and resid 801 through 813 removed outlier: 3.675A pdb=" N ILE C 810 " --> pdb=" O TYR C 806 " (cutoff:3.500A) Processing helix chain 'C' and resid 814 through 828 removed outlier: 3.859A pdb=" N TRP C 818 " --> pdb=" O GLY C 814 " (cutoff:3.500A) Processing helix chain 'C' and resid 830 through 841 removed outlier: 3.502A pdb=" N ALA C 834 " --> pdb=" O LEU C 830 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY C 839 " --> pdb=" O ASP C 835 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA C 840 " --> pdb=" O LYS C 836 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU C 841 " --> pdb=" O LEU C 837 " (cutoff:3.500A) Processing helix chain 'C' and resid 846 through 857 removed outlier: 3.563A pdb=" N ARG C 852 " --> pdb=" O TRP C 848 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR C 857 " --> pdb=" O PHE C 853 " (cutoff:3.500A) Processing helix chain 'C' and resid 864 through 866 No H-bonds generated for 'chain 'C' and resid 864 through 866' Processing helix chain 'C' and resid 867 through 878 removed outlier: 3.686A pdb=" N SER C 873 " --> pdb=" O THR C 869 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASN C 878 " --> pdb=" O SER C 874 " (cutoff:3.500A) Processing helix chain 'C' and resid 881 through 892 removed outlier: 3.744A pdb=" N PHE C 888 " --> pdb=" O LEU C 884 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 892 through 901 removed outlier: 3.573A pdb=" N LEU C 896 " --> pdb=" O ASN C 892 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE C 897 " --> pdb=" O TRP C 893 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN C 898 " --> pdb=" O LYS C 894 " (cutoff:3.500A) Processing helix chain 'C' and resid 906 through 914 Processing helix chain 'C' and resid 920 through 936 removed outlier: 4.251A pdb=" N ASP C 936 " --> pdb=" O LYS C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 941 through 963 removed outlier: 3.565A pdb=" N ALA C 945 " --> pdb=" O SER C 941 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN C 948 " --> pdb=" O ARG C 944 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ALA C 949 " --> pdb=" O ALA C 945 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU C 950 " --> pdb=" O LEU C 946 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LYS C 958 " --> pdb=" O LYS C 954 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TRP C 959 " --> pdb=" O ALA C 955 " (cutoff:3.500A) Processing helix chain 'C' and resid 964 through 974 Processing sheet with id=AA1, first strand: chain 'A' and resid 538 through 540 removed outlier: 3.862A pdb=" N HIS A 563 " --> pdb=" O ILE A 517 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 523 through 525 Processing sheet with id=AA3, first strand: chain 'A' and resid 551 through 552 removed outlier: 6.697A pdb=" N VAL A 625 " --> pdb=" O VAL A 636 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N SER A 638 " --> pdb=" O PHE A 623 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N PHE A 623 " --> pdb=" O SER A 638 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N TYR A 640 " --> pdb=" O CYS A 621 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N CYS A 621 " --> pdb=" O TYR A 640 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ASP A 624 " --> pdb=" O LYS A 590 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N THR A 586 " --> pdb=" O ARG A 628 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 94 through 95 removed outlier: 5.466A pdb=" N ILE C 242 " --> pdb=" O PHE C 276 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 112 through 118 Processing sheet with id=AA6, first strand: chain 'C' and resid 125 through 129 removed outlier: 3.606A pdb=" N TYR C 168 " --> pdb=" O VAL C 163 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N HIS C 172 " --> pdb=" O ARG C 159 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N ARG C 159 " --> pdb=" O HIS C 172 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 199 through 207 removed outlier: 3.505A pdb=" N LEU C 214 " --> pdb=" O SER C 203 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 251 through 253 Processing sheet with id=AA9, first strand: chain 'C' and resid 295 through 300 removed outlier: 5.902A pdb=" N LEU C 306 " --> pdb=" O SER C 348 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N GLN C 350 " --> pdb=" O LEU C 306 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ARG C 308 " --> pdb=" O GLN C 350 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N ALA C 352 " --> pdb=" O ARG C 308 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N TRP C 310 " --> pdb=" O ALA C 352 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N VAL C 367 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ASP C 349 " --> pdb=" O VAL C 367 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N TYR C 369 " --> pdb=" O ASP C 349 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE C 351 " --> pdb=" O TYR C 369 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 406 through 408 Processing sheet with id=AB2, first strand: chain 'C' and resid 615 through 617 Processing sheet with id=AB3, first strand: chain 'C' and resid 594 through 596 Processing sheet with id=AB4, first strand: chain 'C' and resid 603 through 604 339 hydrogen bonds defined for protein. 960 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.05 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1384 1.31 - 1.44: 2491 1.44 - 1.56: 4802 1.56 - 1.69: 1 1.69 - 1.82: 54 Bond restraints: 8732 Sorted by residual: bond pdb=" C ASN C 241 " pdb=" O ASN C 241 " ideal model delta sigma weight residual 1.235 1.187 0.048 1.14e-02 7.69e+03 1.77e+01 bond pdb=" C2 BMA B 3 " pdb=" O2 BMA B 3 " ideal model delta sigma weight residual 1.402 1.440 -0.038 2.00e-02 2.50e+03 3.58e+00 bond pdb=" CB PRO C 558 " pdb=" CG PRO C 558 " ideal model delta sigma weight residual 1.492 1.578 -0.086 5.00e-02 4.00e+02 2.93e+00 bond pdb=" N HIS C 218 " pdb=" CA HIS C 218 " ideal model delta sigma weight residual 1.464 1.485 -0.021 1.25e-02 6.40e+03 2.78e+00 bond pdb=" CA GLN C 220 " pdb=" C GLN C 220 " ideal model delta sigma weight residual 1.523 1.502 0.020 1.23e-02 6.61e+03 2.72e+00 ... (remaining 8727 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.77: 11760 2.77 - 5.53: 146 5.53 - 8.30: 12 8.30 - 11.06: 2 11.06 - 13.83: 1 Bond angle restraints: 11921 Sorted by residual: angle pdb=" N MET C 219 " pdb=" CA MET C 219 " pdb=" C MET C 219 " ideal model delta sigma weight residual 112.92 121.15 -8.23 1.23e+00 6.61e-01 4.47e+01 angle pdb=" C3 BMA B 3 " pdb=" C2 BMA B 3 " pdb=" O2 BMA B 3 " ideal model delta sigma weight residual 112.95 126.78 -13.83 3.00e+00 1.11e-01 2.13e+01 angle pdb=" N ASN C 241 " pdb=" CA ASN C 241 " pdb=" C ASN C 241 " ideal model delta sigma weight residual 108.76 102.46 6.30 1.69e+00 3.50e-01 1.39e+01 angle pdb=" CA PRO C 558 " pdb=" N PRO C 558 " pdb=" CD PRO C 558 " ideal model delta sigma weight residual 112.00 106.89 5.11 1.40e+00 5.10e-01 1.33e+01 angle pdb=" C LEU C 95 " pdb=" N ARG C 96 " pdb=" CA ARG C 96 " ideal model delta sigma weight residual 122.26 125.95 -3.69 1.10e+00 8.26e-01 1.12e+01 ... (remaining 11916 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.13: 4690 22.13 - 44.26: 452 44.26 - 66.39: 113 66.39 - 88.52: 30 88.52 - 110.66: 22 Dihedral angle restraints: 5307 sinusoidal: 2210 harmonic: 3097 Sorted by residual: dihedral pdb=" CA VAL C 108 " pdb=" C VAL C 108 " pdb=" N PHE C 109 " pdb=" CA PHE C 109 " ideal model delta harmonic sigma weight residual 180.00 155.53 24.47 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA THR C 279 " pdb=" C THR C 279 " pdb=" N PRO C 280 " pdb=" CA PRO C 280 " ideal model delta harmonic sigma weight residual 180.00 159.39 20.61 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" C2 FUC B 4 " pdb=" C1 FUC B 4 " pdb=" O5 FUC B 4 " pdb=" C5 FUC B 4 " ideal model delta sinusoidal sigma weight residual 57.68 -52.98 110.66 1 3.00e+01 1.11e-03 1.44e+01 ... (remaining 5304 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.163: 1361 0.163 - 0.326: 6 0.326 - 0.489: 5 0.489 - 0.652: 2 0.652 - 0.815: 2 Chirality restraints: 1376 Sorted by residual: chirality pdb=" C1 FUC B 4 " pdb=" O6 NAG B 1 " pdb=" C2 FUC B 4 " pdb=" O5 FUC B 4 " both_signs ideal model delta sigma weight residual False -2.40 -1.83 -0.57 2.00e-02 2.50e+03 8.26e+02 chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-02 2.50e+03 4.88e+01 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.32 -0.08 2.00e-02 2.50e+03 1.75e+01 ... (remaining 1373 not shown) Planarity restraints: 1516 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1003 " 0.361 2.00e-02 2.50e+03 3.09e-01 1.20e+03 pdb=" C7 NAG C1003 " -0.092 2.00e-02 2.50e+03 pdb=" C8 NAG C1003 " 0.149 2.00e-02 2.50e+03 pdb=" N2 NAG C1003 " -0.548 2.00e-02 2.50e+03 pdb=" O7 NAG C1003 " 0.130 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 701 " -0.313 2.00e-02 2.50e+03 2.74e-01 9.40e+02 pdb=" C7 NAG A 701 " 0.069 2.00e-02 2.50e+03 pdb=" C8 NAG A 701 " -0.061 2.00e-02 2.50e+03 pdb=" N2 NAG A 701 " 0.486 2.00e-02 2.50e+03 pdb=" O7 NAG A 701 " -0.181 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1002 " -0.272 2.00e-02 2.50e+03 2.28e-01 6.47e+02 pdb=" C7 NAG C1002 " 0.079 2.00e-02 2.50e+03 pdb=" C8 NAG C1002 " -0.181 2.00e-02 2.50e+03 pdb=" N2 NAG C1002 " 0.382 2.00e-02 2.50e+03 pdb=" O7 NAG C1002 " -0.008 2.00e-02 2.50e+03 ... (remaining 1513 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1570 2.77 - 3.30: 7900 3.30 - 3.83: 13901 3.83 - 4.37: 15743 4.37 - 4.90: 27235 Nonbonded interactions: 66349 Sorted by model distance: nonbonded pdb=" OG SER C 227 " pdb=" OH TYR C 289 " model vdw 2.237 3.040 nonbonded pdb=" N GLU C 121 " pdb=" OE1 GLU C 121 " model vdw 2.242 3.120 nonbonded pdb=" O LEU C 968 " pdb=" OG1 THR C 972 " model vdw 2.276 3.040 nonbonded pdb=" OG1 THR A 629 " pdb=" O ASN A 632 " model vdw 2.301 3.040 nonbonded pdb=" N THR C 94 " pdb=" O THR C 112 " model vdw 2.303 3.120 ... (remaining 66344 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 'D' selection = chain 'E' } 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: 4.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.250 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 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 : 0.005 0.086 8747 Z= 0.217 Angle : 0.780 13.831 11963 Z= 0.410 Chirality : 0.065 0.815 1376 Planarity : 0.016 0.309 1509 Dihedral : 20.381 110.655 3294 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.60 % Allowed : 27.77 % Favored : 69.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.24), residues: 1045 helix: 0.30 (0.26), residues: 392 sheet: -0.71 (0.35), residues: 196 loop : -1.19 (0.26), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 744 TYR 0.012 0.002 TYR C 643 PHE 0.027 0.001 PHE C 497 TRP 0.036 0.002 TRP C 310 HIS 0.005 0.001 HIS C 512 Details of bonding type rmsd covalent geometry : bond 0.00455 ( 8732) covalent geometry : angle 0.75487 (11921) SS BOND : bond 0.00233 ( 3) SS BOND : angle 0.51259 ( 6) hydrogen bonds : bond 0.21214 ( 339) hydrogen bonds : angle 7.10092 ( 960) link_BETA1-4 : bond 0.00350 ( 4) link_BETA1-4 : angle 2.35157 ( 12) link_BETA1-6 : bond 0.00051 ( 1) link_BETA1-6 : angle 2.64018 ( 3) link_NAG-ASN : bond 0.01173 ( 7) link_NAG-ASN : angle 4.29670 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 143 time to evaluate : 0.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 613 SER cc_start: 0.8129 (p) cc_final: 0.7772 (t) outliers start: 24 outliers final: 9 residues processed: 164 average time/residue: 0.4193 time to fit residues: 74.4737 Evaluate side-chains 81 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 564 THR Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 636 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 20.0000 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 20.0000 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 608 ASN ** C 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 152 HIS C 317 ASN C 363 ASN C 417 ASN C 512 HIS C 571 GLN C 573 HIS ** C 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 669 GLN ** C 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN C 791 ASN C 808 ASN C 861 ASN C 925 GLN C 933 ASN C 934 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.107852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.080241 restraints weight = 24755.018| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 4.72 r_work: 0.3327 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8747 Z= 0.212 Angle : 0.768 18.643 11963 Z= 0.377 Chirality : 0.052 0.522 1376 Planarity : 0.005 0.067 1509 Dihedral : 11.086 121.434 1385 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 6.83 % Allowed : 27.11 % Favored : 66.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.25), residues: 1045 helix: 0.56 (0.25), residues: 416 sheet: -0.61 (0.37), residues: 194 loop : -1.03 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 116 TYR 0.017 0.002 TYR C 510 PHE 0.028 0.002 PHE C 497 TRP 0.024 0.002 TRP C 310 HIS 0.007 0.001 HIS C 512 Details of bonding type rmsd covalent geometry : bond 0.00489 ( 8732) covalent geometry : angle 0.72882 (11921) SS BOND : bond 0.00388 ( 3) SS BOND : angle 0.74151 ( 6) hydrogen bonds : bond 0.05391 ( 339) hydrogen bonds : angle 5.13341 ( 960) link_BETA1-4 : bond 0.00447 ( 4) link_BETA1-4 : angle 1.80494 ( 12) link_BETA1-6 : bond 0.00427 ( 1) link_BETA1-6 : angle 2.39959 ( 3) link_NAG-ASN : bond 0.00842 ( 7) link_NAG-ASN : angle 5.62842 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 78 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 517 ILE cc_start: 0.8224 (pp) cc_final: 0.8008 (pp) REVERT: A 520 ASP cc_start: 0.9060 (p0) cc_final: 0.8832 (p0) REVERT: A 523 MET cc_start: 0.8420 (OUTLIER) cc_final: 0.6923 (mpp) REVERT: C 79 VAL cc_start: 0.8994 (OUTLIER) cc_final: 0.8775 (m) REVERT: C 119 CYS cc_start: 0.8724 (m) cc_final: 0.8053 (m) REVERT: C 142 MET cc_start: 0.1789 (ptp) cc_final: 0.1158 (ppp) REVERT: C 226 LYS cc_start: 0.7261 (OUTLIER) cc_final: 0.7028 (mtpm) REVERT: C 787 GLN cc_start: 0.6849 (OUTLIER) cc_final: 0.6554 (mp10) outliers start: 63 outliers final: 17 residues processed: 130 average time/residue: 0.3316 time to fit residues: 47.4617 Evaluate side-chains 85 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 64 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 226 LYS Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 537 THR Chi-restraints excluded: chain C residue 561 THR Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 598 SER Chi-restraints excluded: chain C residue 712 SER Chi-restraints excluded: chain C residue 735 VAL Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 831 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 28 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 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 516 ASN A 634 GLN ** C 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 HIS C 417 ASN C 571 GLN C 607 HIS ** C 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 652 GLN C 691 ASN ** C 795 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 832 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.106040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.078296 restraints weight = 24734.263| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 5.08 r_work: 0.3298 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8747 Z= 0.211 Angle : 0.687 9.392 11963 Z= 0.347 Chirality : 0.048 0.194 1376 Planarity : 0.005 0.053 1509 Dihedral : 8.465 116.739 1376 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 7.05 % Allowed : 26.03 % Favored : 66.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.25), residues: 1045 helix: 0.79 (0.25), residues: 417 sheet: -0.41 (0.38), residues: 183 loop : -1.04 (0.27), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 637 TYR 0.018 0.001 TYR C 510 PHE 0.025 0.002 PHE C 497 TRP 0.018 0.001 TRP C 364 HIS 0.003 0.001 HIS C 129 Details of bonding type rmsd covalent geometry : bond 0.00488 ( 8732) covalent geometry : angle 0.67745 (11921) SS BOND : bond 0.00378 ( 3) SS BOND : angle 0.54132 ( 6) hydrogen bonds : bond 0.05625 ( 339) hydrogen bonds : angle 4.86599 ( 960) link_BETA1-4 : bond 0.00547 ( 4) link_BETA1-4 : angle 2.00673 ( 12) link_BETA1-6 : bond 0.00415 ( 1) link_BETA1-6 : angle 0.51456 ( 3) link_NAG-ASN : bond 0.01080 ( 7) link_NAG-ASN : angle 2.35880 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 67 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 520 ASP cc_start: 0.9069 (p0) cc_final: 0.8840 (p0) REVERT: A 567 LYS cc_start: 0.7750 (mtmt) cc_final: 0.6975 (mmmt) REVERT: C 119 CYS cc_start: 0.8732 (OUTLIER) cc_final: 0.7997 (m) REVERT: C 142 MET cc_start: 0.2173 (ptp) cc_final: 0.1572 (tmt) REVERT: C 290 ILE cc_start: 0.8640 (mm) cc_final: 0.8286 (tp) REVERT: C 534 LYS cc_start: 0.9289 (mtpt) cc_final: 0.9059 (ptmt) outliers start: 65 outliers final: 29 residues processed: 122 average time/residue: 0.3176 time to fit residues: 43.0045 Evaluate side-chains 88 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 58 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 543 MET Chi-restraints excluded: chain A residue 564 SER Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 119 CYS Chi-restraints excluded: chain C residue 141 HIS Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 537 THR Chi-restraints excluded: chain C residue 561 THR Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 564 THR Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 570 SER Chi-restraints excluded: chain C residue 598 SER Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain C residue 712 SER Chi-restraints excluded: chain C residue 735 VAL Chi-restraints excluded: chain C residue 755 THR Chi-restraints excluded: chain C residue 826 LEU Chi-restraints excluded: chain C residue 863 ILE Chi-restraints excluded: chain C residue 883 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 19 optimal weight: 10.0000 chunk 83 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 chunk 68 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 1 optimal weight: 8.9990 chunk 13 optimal weight: 20.0000 chunk 12 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 634 GLN ** C 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 HIS C 139 GLN C 417 ASN C 647 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.102620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.074887 restraints weight = 25351.519| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 4.98 r_work: 0.3232 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.088 8747 Z= 0.323 Angle : 0.781 9.159 11963 Z= 0.403 Chirality : 0.051 0.190 1376 Planarity : 0.005 0.047 1509 Dihedral : 8.663 115.086 1376 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 7.70 % Allowed : 25.92 % Favored : 66.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.25), residues: 1045 helix: 0.41 (0.25), residues: 416 sheet: -0.97 (0.37), residues: 187 loop : -1.21 (0.27), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 225 TYR 0.029 0.002 TYR C 91 PHE 0.032 0.003 PHE C 497 TRP 0.030 0.002 TRP C 310 HIS 0.009 0.001 HIS C 129 Details of bonding type rmsd covalent geometry : bond 0.00754 ( 8732) covalent geometry : angle 0.76987 (11921) SS BOND : bond 0.00537 ( 3) SS BOND : angle 0.78817 ( 6) hydrogen bonds : bond 0.06761 ( 339) hydrogen bonds : angle 5.17402 ( 960) link_BETA1-4 : bond 0.00372 ( 4) link_BETA1-4 : angle 2.21295 ( 12) link_BETA1-6 : bond 0.00831 ( 1) link_BETA1-6 : angle 1.43251 ( 3) link_NAG-ASN : bond 0.00841 ( 7) link_NAG-ASN : angle 2.84324 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 60 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 520 ASP cc_start: 0.8972 (p0) cc_final: 0.8705 (p0) REVERT: A 567 LYS cc_start: 0.7822 (mtmt) cc_final: 0.7560 (mtpp) REVERT: C 79 VAL cc_start: 0.9102 (OUTLIER) cc_final: 0.8882 (m) REVERT: C 119 CYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8103 (m) REVERT: C 142 MET cc_start: 0.3509 (ptp) cc_final: 0.2826 (tmt) REVERT: C 190 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.8381 (mp10) REVERT: C 219 MET cc_start: 0.8975 (OUTLIER) cc_final: 0.8772 (tpp) REVERT: C 290 ILE cc_start: 0.8689 (mm) cc_final: 0.8285 (tp) REVERT: C 511 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8364 (mp) REVERT: C 787 GLN cc_start: 0.6986 (OUTLIER) cc_final: 0.6641 (mp10) REVERT: C 817 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.6909 (mp0) outliers start: 71 outliers final: 32 residues processed: 122 average time/residue: 0.3419 time to fit residues: 45.9373 Evaluate side-chains 93 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 54 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 543 MET Chi-restraints excluded: chain A residue 564 SER Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 119 CYS Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 141 HIS Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 190 GLN Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 511 LEU Chi-restraints excluded: chain C residue 537 THR Chi-restraints excluded: chain C residue 561 THR Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 564 THR Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 570 SER Chi-restraints excluded: chain C residue 598 SER Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain C residue 712 SER Chi-restraints excluded: chain C residue 735 VAL Chi-restraints excluded: chain C residue 755 THR Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 817 GLU Chi-restraints excluded: chain C residue 826 LEU Chi-restraints excluded: chain C residue 831 VAL Chi-restraints excluded: chain C residue 863 ILE Chi-restraints excluded: chain C residue 883 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 99 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 102 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 516 ASN A 563 HIS C 113 ASN C 138 HIS C 417 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.105558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.078213 restraints weight = 25259.727| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 5.15 r_work: 0.3297 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8747 Z= 0.133 Angle : 0.640 10.221 11963 Z= 0.325 Chirality : 0.047 0.245 1376 Planarity : 0.004 0.042 1509 Dihedral : 7.775 104.017 1376 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 5.64 % Allowed : 29.39 % Favored : 64.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.25), residues: 1045 helix: 0.89 (0.25), residues: 422 sheet: -0.73 (0.38), residues: 177 loop : -1.08 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 628 TYR 0.014 0.001 TYR C 510 PHE 0.019 0.001 PHE C 497 TRP 0.017 0.001 TRP C 310 HIS 0.005 0.001 HIS C 395 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 8732) covalent geometry : angle 0.63156 (11921) SS BOND : bond 0.00257 ( 3) SS BOND : angle 0.66839 ( 6) hydrogen bonds : bond 0.04634 ( 339) hydrogen bonds : angle 4.69852 ( 960) link_BETA1-4 : bond 0.00376 ( 4) link_BETA1-4 : angle 1.60320 ( 12) link_BETA1-6 : bond 0.01194 ( 1) link_BETA1-6 : angle 1.73841 ( 3) link_NAG-ASN : bond 0.00648 ( 7) link_NAG-ASN : angle 2.13128 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 64 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 548 THR cc_start: 0.5525 (OUTLIER) cc_final: 0.4961 (m) REVERT: A 567 LYS cc_start: 0.7794 (mtmt) cc_final: 0.6892 (mmmt) REVERT: A 635 VAL cc_start: 0.8163 (OUTLIER) cc_final: 0.7772 (t) REVERT: A 643 TYR cc_start: 0.7382 (p90) cc_final: 0.7165 (p90) REVERT: C 117 PHE cc_start: 0.5972 (p90) cc_final: 0.5746 (p90) REVERT: C 119 CYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8001 (m) REVERT: C 142 MET cc_start: 0.3332 (ptp) cc_final: 0.2848 (tmt) REVERT: C 290 ILE cc_start: 0.8587 (mm) cc_final: 0.8215 (tp) REVERT: C 534 LYS cc_start: 0.9170 (mtmt) cc_final: 0.8951 (ptmt) outliers start: 52 outliers final: 23 residues processed: 107 average time/residue: 0.4103 time to fit residues: 47.8905 Evaluate side-chains 84 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 58 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 564 SER Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 119 CYS Chi-restraints excluded: chain C residue 141 HIS Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 561 THR Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 564 THR Chi-restraints excluded: chain C residue 570 SER Chi-restraints excluded: chain C residue 598 SER Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain C residue 712 SER Chi-restraints excluded: chain C residue 735 VAL Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 826 LEU Chi-restraints excluded: chain C residue 863 ILE Chi-restraints excluded: chain C residue 883 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 97 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 100 optimal weight: 20.0000 chunk 101 optimal weight: 3.9990 chunk 32 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 9 optimal weight: 0.8980 chunk 42 optimal weight: 10.0000 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 HIS A 632 ASN C 138 HIS C 417 ASN ** C 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.103354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.076193 restraints weight = 25292.409| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 4.90 r_work: 0.3249 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8747 Z= 0.229 Angle : 0.698 9.620 11963 Z= 0.355 Chirality : 0.048 0.236 1376 Planarity : 0.005 0.040 1509 Dihedral : 7.989 107.751 1375 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 5.75 % Allowed : 28.85 % Favored : 65.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.25), residues: 1045 helix: 0.77 (0.25), residues: 422 sheet: -0.88 (0.37), residues: 187 loop : -1.06 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 630 TYR 0.020 0.002 TYR C 91 PHE 0.026 0.002 PHE C 497 TRP 0.020 0.002 TRP C 364 HIS 0.006 0.001 HIS C 129 Details of bonding type rmsd covalent geometry : bond 0.00534 ( 8732) covalent geometry : angle 0.68893 (11921) SS BOND : bond 0.00381 ( 3) SS BOND : angle 0.72955 ( 6) hydrogen bonds : bond 0.05523 ( 339) hydrogen bonds : angle 4.81804 ( 960) link_BETA1-4 : bond 0.00379 ( 4) link_BETA1-4 : angle 1.90162 ( 12) link_BETA1-6 : bond 0.01047 ( 1) link_BETA1-6 : angle 1.55953 ( 3) link_NAG-ASN : bond 0.00594 ( 7) link_NAG-ASN : angle 2.35505 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 56 time to evaluate : 0.349 Fit side-chains REVERT: A 523 MET cc_start: 0.8521 (OUTLIER) cc_final: 0.8025 (mpp) REVERT: A 547 ASN cc_start: 0.8238 (m-40) cc_final: 0.7928 (p0) REVERT: A 632 ASN cc_start: 0.3930 (OUTLIER) cc_final: 0.3336 (p0) REVERT: A 643 TYR cc_start: 0.7676 (p90) cc_final: 0.7425 (p90) REVERT: C 185 MET cc_start: 0.5978 (tpt) cc_final: 0.5454 (tpt) REVERT: C 290 ILE cc_start: 0.8677 (mm) cc_final: 0.8286 (tp) REVERT: C 454 ASP cc_start: 0.9250 (OUTLIER) cc_final: 0.9045 (m-30) REVERT: C 534 LYS cc_start: 0.9193 (mtmt) cc_final: 0.8948 (ptmt) outliers start: 53 outliers final: 31 residues processed: 101 average time/residue: 0.3898 time to fit residues: 43.2767 Evaluate side-chains 86 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 52 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 564 SER Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 620 ASN Chi-restraints excluded: chain A residue 632 ASN Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 119 CYS Chi-restraints excluded: chain C residue 141 HIS Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 226 LYS Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 537 THR Chi-restraints excluded: chain C residue 561 THR Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 564 THR Chi-restraints excluded: chain C residue 570 SER Chi-restraints excluded: chain C residue 598 SER Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain C residue 712 SER Chi-restraints excluded: chain C residue 735 VAL Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 826 LEU Chi-restraints excluded: chain C residue 855 SER Chi-restraints excluded: chain C residue 863 ILE Chi-restraints excluded: chain C residue 883 THR Chi-restraints excluded: chain C residue 966 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 33 optimal weight: 5.9990 chunk 70 optimal weight: 0.5980 chunk 75 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 96 optimal weight: 7.9990 chunk 31 optimal weight: 4.9990 chunk 51 optimal weight: 0.0010 chunk 40 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 83 optimal weight: 0.0980 overall best weight: 0.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 HIS A 634 GLN C 218 HIS C 417 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.106673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.079240 restraints weight = 25466.533| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 5.55 r_work: 0.3327 rms_B_bonded: 5.11 restraints_weight: 2.0000 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8747 Z= 0.117 Angle : 0.653 10.050 11963 Z= 0.326 Chirality : 0.046 0.268 1376 Planarity : 0.004 0.038 1509 Dihedral : 7.388 98.423 1375 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 4.01 % Allowed : 30.59 % Favored : 65.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.26), residues: 1045 helix: 1.27 (0.25), residues: 416 sheet: -0.73 (0.37), residues: 193 loop : -1.02 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 630 TYR 0.012 0.001 TYR C 510 PHE 0.024 0.001 PHE C 117 TRP 0.017 0.001 TRP C 788 HIS 0.005 0.001 HIS C 395 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 8732) covalent geometry : angle 0.64660 (11921) SS BOND : bond 0.00178 ( 3) SS BOND : angle 0.66693 ( 6) hydrogen bonds : bond 0.03958 ( 339) hydrogen bonds : angle 4.52065 ( 960) link_BETA1-4 : bond 0.00436 ( 4) link_BETA1-4 : angle 1.43707 ( 12) link_BETA1-6 : bond 0.01481 ( 1) link_BETA1-6 : angle 2.11227 ( 3) link_NAG-ASN : bond 0.00657 ( 7) link_NAG-ASN : angle 1.85444 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 66 time to evaluate : 0.298 Fit side-chains revert: symmetry clash REVERT: A 523 MET cc_start: 0.8524 (mpp) cc_final: 0.8005 (mpp) REVERT: A 547 ASN cc_start: 0.8014 (m-40) cc_final: 0.7676 (p0) REVERT: A 567 LYS cc_start: 0.7903 (mtmt) cc_final: 0.7540 (mtpp) REVERT: C 119 CYS cc_start: 0.8784 (OUTLIER) cc_final: 0.8014 (m) REVERT: C 226 LYS cc_start: 0.7480 (OUTLIER) cc_final: 0.7193 (mtpm) REVERT: C 290 ILE cc_start: 0.8542 (mm) cc_final: 0.8147 (tp) REVERT: C 534 LYS cc_start: 0.9174 (mtmt) cc_final: 0.8946 (ptmt) outliers start: 37 outliers final: 20 residues processed: 96 average time/residue: 0.3954 time to fit residues: 41.2791 Evaluate side-chains 79 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 57 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 119 CYS Chi-restraints excluded: chain C residue 141 HIS Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 226 LYS Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 570 SER Chi-restraints excluded: chain C residue 598 SER Chi-restraints excluded: chain C residue 712 SER Chi-restraints excluded: chain C residue 717 MET Chi-restraints excluded: chain C residue 735 VAL Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 826 LEU Chi-restraints excluded: chain C residue 863 ILE Chi-restraints excluded: chain C residue 920 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 63 optimal weight: 8.9990 chunk 95 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 chunk 7 optimal weight: 0.0980 chunk 14 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 100 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 HIS A 632 ASN C 138 HIS C 417 ASN C 496 ASN ** C 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.103832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.076754 restraints weight = 25317.187| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 4.96 r_work: 0.3267 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.3802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8747 Z= 0.209 Angle : 0.697 10.314 11963 Z= 0.353 Chirality : 0.048 0.264 1376 Planarity : 0.004 0.038 1509 Dihedral : 7.760 103.769 1375 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 4.56 % Allowed : 30.69 % Favored : 64.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.26), residues: 1045 helix: 1.02 (0.25), residues: 422 sheet: -0.68 (0.37), residues: 188 loop : -1.06 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 116 TYR 0.018 0.001 TYR A 643 PHE 0.025 0.002 PHE C 497 TRP 0.019 0.001 TRP C 364 HIS 0.005 0.001 HIS C 129 Details of bonding type rmsd covalent geometry : bond 0.00490 ( 8732) covalent geometry : angle 0.68855 (11921) SS BOND : bond 0.00349 ( 3) SS BOND : angle 0.67479 ( 6) hydrogen bonds : bond 0.05271 ( 339) hydrogen bonds : angle 4.71686 ( 960) link_BETA1-4 : bond 0.00327 ( 4) link_BETA1-4 : angle 1.79022 ( 12) link_BETA1-6 : bond 0.01088 ( 1) link_BETA1-6 : angle 1.65291 ( 3) link_NAG-ASN : bond 0.00529 ( 7) link_NAG-ASN : angle 2.28933 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 56 time to evaluate : 0.378 Fit side-chains REVERT: A 523 MET cc_start: 0.8524 (mpp) cc_final: 0.8049 (mpp) REVERT: A 547 ASN cc_start: 0.8122 (m-40) cc_final: 0.7843 (p0) REVERT: A 567 LYS cc_start: 0.7816 (mtmt) cc_final: 0.7457 (mtpp) REVERT: C 219 MET cc_start: 0.8709 (mmm) cc_final: 0.8394 (mmm) REVERT: C 534 LYS cc_start: 0.9179 (mtmt) cc_final: 0.8929 (ptmt) REVERT: C 929 GLN cc_start: 0.7717 (OUTLIER) cc_final: 0.7453 (tm-30) outliers start: 42 outliers final: 29 residues processed: 91 average time/residue: 0.4004 time to fit residues: 39.8944 Evaluate side-chains 84 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 54 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 564 SER Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 620 ASN Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 119 CYS Chi-restraints excluded: chain C residue 141 HIS Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 226 LYS Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 470 ASN Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 564 THR Chi-restraints excluded: chain C residue 570 SER Chi-restraints excluded: chain C residue 598 SER Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain C residue 712 SER Chi-restraints excluded: chain C residue 735 VAL Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 826 LEU Chi-restraints excluded: chain C residue 863 ILE Chi-restraints excluded: chain C residue 883 THR Chi-restraints excluded: chain C residue 920 THR Chi-restraints excluded: chain C residue 929 GLN Chi-restraints excluded: chain C residue 966 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 58 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 21 optimal weight: 0.3980 chunk 89 optimal weight: 0.0470 chunk 24 optimal weight: 0.6980 chunk 28 optimal weight: 9.9990 chunk 53 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 HIS A 632 ASN C 417 ASN C 496 ASN ** C 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.107660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.080431 restraints weight = 25366.400| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 5.55 r_work: 0.3338 rms_B_bonded: 5.17 restraints_weight: 2.0000 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8747 Z= 0.114 Angle : 0.648 9.622 11963 Z= 0.322 Chirality : 0.045 0.267 1376 Planarity : 0.004 0.038 1509 Dihedral : 7.066 92.091 1375 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.36 % Allowed : 32.32 % Favored : 64.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.26), residues: 1045 helix: 1.36 (0.25), residues: 417 sheet: -0.50 (0.38), residues: 189 loop : -1.12 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 300 TYR 0.014 0.001 TYR A 643 PHE 0.020 0.001 PHE C 117 TRP 0.020 0.001 TRP C 592 HIS 0.005 0.001 HIS C 395 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 8732) covalent geometry : angle 0.64173 (11921) SS BOND : bond 0.00159 ( 3) SS BOND : angle 0.72762 ( 6) hydrogen bonds : bond 0.03631 ( 339) hydrogen bonds : angle 4.46618 ( 960) link_BETA1-4 : bond 0.00418 ( 4) link_BETA1-4 : angle 1.24583 ( 12) link_BETA1-6 : bond 0.01567 ( 1) link_BETA1-6 : angle 2.34195 ( 3) link_NAG-ASN : bond 0.00673 ( 7) link_NAG-ASN : angle 1.85012 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 66 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 523 MET cc_start: 0.8540 (mpp) cc_final: 0.8013 (mpp) REVERT: A 532 ILE cc_start: 0.6459 (mt) cc_final: 0.6257 (mp) REVERT: A 547 ASN cc_start: 0.8038 (m-40) cc_final: 0.7772 (p0) REVERT: A 567 LYS cc_start: 0.7760 (mtmt) cc_final: 0.7362 (mtpp) REVERT: C 100 THR cc_start: 0.8962 (OUTLIER) cc_final: 0.8671 (p) REVERT: C 119 CYS cc_start: 0.8722 (m) cc_final: 0.7864 (m) REVERT: C 226 LYS cc_start: 0.7332 (OUTLIER) cc_final: 0.7055 (mtpm) REVERT: C 290 ILE cc_start: 0.8431 (OUTLIER) cc_final: 0.8043 (tp) REVERT: C 534 LYS cc_start: 0.9160 (mtmt) cc_final: 0.8923 (ptmt) REVERT: C 539 LYS cc_start: 0.9421 (OUTLIER) cc_final: 0.9061 (mmmm) outliers start: 31 outliers final: 14 residues processed: 92 average time/residue: 0.3913 time to fit residues: 39.2842 Evaluate side-chains 76 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 58 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 226 LYS Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 539 LYS Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 570 SER Chi-restraints excluded: chain C residue 598 SER Chi-restraints excluded: chain C residue 712 SER Chi-restraints excluded: chain C residue 717 MET Chi-restraints excluded: chain C residue 735 VAL Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 920 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 89 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 chunk 69 optimal weight: 7.9990 chunk 82 optimal weight: 0.0970 chunk 103 optimal weight: 0.9980 chunk 60 optimal weight: 0.0370 chunk 77 optimal weight: 3.9990 chunk 75 optimal weight: 0.6980 chunk 61 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 overall best weight: 0.5256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 HIS C 417 ASN C 496 ASN ** C 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.107900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.081125 restraints weight = 25235.376| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 5.10 r_work: 0.3347 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.4069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8747 Z= 0.115 Angle : 0.664 11.828 11963 Z= 0.325 Chirality : 0.045 0.182 1376 Planarity : 0.004 0.037 1509 Dihedral : 6.552 78.626 1375 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.84 % Allowed : 34.16 % Favored : 63.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.26), residues: 1045 helix: 1.45 (0.26), residues: 417 sheet: -0.40 (0.37), residues: 194 loop : -1.10 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 225 TYR 0.013 0.001 TYR C 91 PHE 0.016 0.001 PHE C 497 TRP 0.017 0.001 TRP C 592 HIS 0.006 0.001 HIS C 395 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 8732) covalent geometry : angle 0.65828 (11921) SS BOND : bond 0.00152 ( 3) SS BOND : angle 0.66490 ( 6) hydrogen bonds : bond 0.03583 ( 339) hydrogen bonds : angle 4.41852 ( 960) link_BETA1-4 : bond 0.00285 ( 4) link_BETA1-4 : angle 1.37793 ( 12) link_BETA1-6 : bond 0.01633 ( 1) link_BETA1-6 : angle 2.42783 ( 3) link_NAG-ASN : bond 0.00516 ( 7) link_NAG-ASN : angle 1.85683 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 523 MET cc_start: 0.8479 (mpp) cc_final: 0.8068 (mpp) REVERT: A 547 ASN cc_start: 0.8212 (m-40) cc_final: 0.7937 (p0) REVERT: A 567 LYS cc_start: 0.7594 (mtmt) cc_final: 0.7230 (mtpp) REVERT: C 100 THR cc_start: 0.8965 (OUTLIER) cc_final: 0.8669 (p) REVERT: C 119 CYS cc_start: 0.8690 (m) cc_final: 0.7853 (m) REVERT: C 226 LYS cc_start: 0.7317 (OUTLIER) cc_final: 0.7036 (mtpm) REVERT: C 290 ILE cc_start: 0.8463 (mm) cc_final: 0.8099 (tp) REVERT: C 417 ASN cc_start: 0.8664 (OUTLIER) cc_final: 0.8441 (t0) REVERT: C 534 LYS cc_start: 0.9141 (mtmt) cc_final: 0.8898 (ptmt) outliers start: 17 outliers final: 10 residues processed: 80 average time/residue: 0.4146 time to fit residues: 36.0436 Evaluate side-chains 74 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 226 LYS Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 417 ASN Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 570 SER Chi-restraints excluded: chain C residue 735 VAL Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 920 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 0.0980 chunk 103 optimal weight: 0.5980 chunk 66 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 11 optimal weight: 9.9990 chunk 79 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 HIS C 417 ASN C 496 ASN ** C 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.106256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.079303 restraints weight = 25352.337| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 5.12 r_work: 0.3314 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.4073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8747 Z= 0.154 Angle : 0.695 13.751 11963 Z= 0.342 Chirality : 0.046 0.157 1376 Planarity : 0.004 0.037 1509 Dihedral : 6.368 70.346 1375 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.92 % Favored : 95.98 % Rotamer: Outliers : 2.28 % Allowed : 33.62 % Favored : 64.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.26), residues: 1045 helix: 1.44 (0.26), residues: 417 sheet: -0.58 (0.37), residues: 205 loop : -1.09 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 628 TYR 0.015 0.001 TYR C 323 PHE 0.021 0.001 PHE C 497 TRP 0.013 0.001 TRP C 592 HIS 0.004 0.001 HIS C 395 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 8732) covalent geometry : angle 0.68878 (11921) SS BOND : bond 0.00250 ( 3) SS BOND : angle 0.60008 ( 6) hydrogen bonds : bond 0.04186 ( 339) hydrogen bonds : angle 4.45127 ( 960) link_BETA1-4 : bond 0.00344 ( 4) link_BETA1-4 : angle 1.48058 ( 12) link_BETA1-6 : bond 0.01854 ( 1) link_BETA1-6 : angle 2.45454 ( 3) link_NAG-ASN : bond 0.00473 ( 7) link_NAG-ASN : angle 2.00459 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2993.49 seconds wall clock time: 51 minutes 38.63 seconds (3098.63 seconds total)