Starting phenix.real_space_refine on Fri Sep 19 12:11:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7stm_25433/09_2025/7stm_25433_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7stm_25433/09_2025/7stm_25433.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7stm_25433/09_2025/7stm_25433_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7stm_25433/09_2025/7stm_25433_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7stm_25433/09_2025/7stm_25433.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7stm_25433/09_2025/7stm_25433.map" } resolution = 3.02 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 12 5.49 5 Mg 2 5.21 5 S 56 5.16 5 C 8474 2.51 5 N 2068 2.21 5 O 2328 1.98 5 H 12100 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25040 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 12321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 801, 12321 Classifications: {'peptide': 801} Link IDs: {'PTRANS': 25, 'TRANS': 775} Chain breaks: 1 Unresolved non-hydrogen bonds: 204 Unresolved non-hydrogen angles: 250 Unresolved non-hydrogen dihedrals: 158 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 11, 'GLU:plan': 11, 'ARG:plan': 6, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 122 Chain: "A" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 199 Unusual residues: {' MG': 1, '3PE': 4, 'UD1': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 45 Restraints were copied for chains: B Time building chain proxies: 19.27, per 1000 atoms: 0.77 Number of scatterers: 25040 At special positions: 0 Unit cell: (91.8, 132.84, 119.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 56 16.00 P 12 15.00 Mg 2 11.99 O 2328 8.00 N 2068 7.00 C 8474 6.00 H 12100 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.61 Conformation dependent library (CDL) restraints added in 813.1 milliseconds Enol-peptide restraints added in 1.2 microseconds 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3012 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 6 sheets defined 61.7% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 142 through 144 No H-bonds generated for 'chain 'A' and resid 142 through 144' Processing helix chain 'A' and resid 145 through 155 Processing helix chain 'A' and resid 242 through 246 removed outlier: 3.703A pdb=" N GLY A 245 " --> pdb=" O GLY A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 261 removed outlier: 3.503A pdb=" N PHE A 261 " --> pdb=" O LEU A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 278 Processing helix chain 'A' and resid 288 through 292 Processing helix chain 'A' and resid 299 through 304 removed outlier: 3.744A pdb=" N TYR A 304 " --> pdb=" O ARG A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 343 removed outlier: 3.534A pdb=" N LEU A 326 " --> pdb=" O ASP A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 355 removed outlier: 3.598A pdb=" N LYS A 355 " --> pdb=" O ASP A 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 352 through 355' Processing helix chain 'A' and resid 370 through 381 Processing helix chain 'A' and resid 439 through 450 removed outlier: 3.871A pdb=" N ASN A 443 " --> pdb=" O ALA A 439 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER A 444 " --> pdb=" O LYS A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 457 Processing helix chain 'A' and resid 473 through 485 removed outlier: 3.860A pdb=" N ASP A 485 " --> pdb=" O GLU A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 532 removed outlier: 4.850A pdb=" N LYS A 525 " --> pdb=" O ASN A 521 " (cutoff:3.500A) Proline residue: A 526 - end of helix Processing helix chain 'A' and resid 545 through 550 removed outlier: 3.663A pdb=" N LEU A 549 " --> pdb=" O ARG A 545 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN A 550 " --> pdb=" O PHE A 546 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 545 through 550' Processing helix chain 'A' and resid 557 through 569 removed outlier: 3.996A pdb=" N GLY A 565 " --> pdb=" O LYS A 561 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLU A 566 " --> pdb=" O TYR A 562 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE A 567 " --> pdb=" O PHE A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 590 Processing helix chain 'A' and resid 593 through 598 Processing helix chain 'A' and resid 599 through 603 removed outlier: 3.745A pdb=" N GLU A 603 " --> pdb=" O TYR A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 613 removed outlier: 3.982A pdb=" N CYS A 608 " --> pdb=" O ASP A 604 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N PHE A 609 " --> pdb=" O ARG A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 661 Processing helix chain 'A' and resid 662 through 668 Processing helix chain 'A' and resid 671 through 694 Processing helix chain 'A' and resid 694 through 710 removed outlier: 3.557A pdb=" N LEU A 710 " --> pdb=" O LEU A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 745 Processing helix chain 'A' and resid 750 through 787 removed outlier: 3.988A pdb=" N TYR A 754 " --> pdb=" O THR A 750 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR A 784 " --> pdb=" O ILE A 780 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY A 787 " --> pdb=" O ILE A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 798 removed outlier: 3.698A pdb=" N PHE A 795 " --> pdb=" O THR A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 822 removed outlier: 4.031A pdb=" N ALA A 807 " --> pdb=" O ASP A 803 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N THR A 808 " --> pdb=" O LEU A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 831 Processing helix chain 'A' and resid 831 through 853 Proline residue: A 840 - end of helix removed outlier: 3.808A pdb=" N LEU A 846 " --> pdb=" O TYR A 842 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASN A 847 " --> pdb=" O VAL A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 905 removed outlier: 3.663A pdb=" N ASP A 905 " --> pdb=" O GLU A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 946 removed outlier: 4.074A pdb=" N TYR A 921 " --> pdb=" O ASN A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 954 removed outlier: 4.213A pdb=" N ASN A 951 " --> pdb=" O GLY A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 1002 removed outlier: 4.239A pdb=" N ALA A 960 " --> pdb=" O ALA A 956 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N ASN A 961 " --> pdb=" O THR A 957 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER A 964 " --> pdb=" O ALA A 960 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASN A 965 " --> pdb=" O ASN A 961 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 144 No H-bonds generated for 'chain 'B' and resid 142 through 144' Processing helix chain 'B' and resid 145 through 155 Processing helix chain 'B' and resid 242 through 246 removed outlier: 3.703A pdb=" N GLY B 245 " --> pdb=" O GLY B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 261 removed outlier: 3.503A pdb=" N PHE B 261 " --> pdb=" O LEU B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 278 Processing helix chain 'B' and resid 288 through 292 Processing helix chain 'B' and resid 299 through 304 removed outlier: 3.744A pdb=" N TYR B 304 " --> pdb=" O ARG B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 343 removed outlier: 3.534A pdb=" N LEU B 326 " --> pdb=" O ASP B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 355 removed outlier: 3.598A pdb=" N LYS B 355 " --> pdb=" O ASP B 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 352 through 355' Processing helix chain 'B' and resid 370 through 381 Processing helix chain 'B' and resid 439 through 450 removed outlier: 3.871A pdb=" N ASN B 443 " --> pdb=" O ALA B 439 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER B 444 " --> pdb=" O LYS B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 457 Processing helix chain 'B' and resid 473 through 485 removed outlier: 3.860A pdb=" N ASP B 485 " --> pdb=" O GLU B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 532 removed outlier: 4.850A pdb=" N LYS B 525 " --> pdb=" O ASN B 521 " (cutoff:3.500A) Proline residue: B 526 - end of helix Processing helix chain 'B' and resid 545 through 550 removed outlier: 3.663A pdb=" N LEU B 549 " --> pdb=" O ARG B 545 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLN B 550 " --> pdb=" O PHE B 546 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 545 through 550' Processing helix chain 'B' and resid 557 through 569 removed outlier: 3.996A pdb=" N GLY B 565 " --> pdb=" O LYS B 561 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLU B 566 " --> pdb=" O TYR B 562 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE B 567 " --> pdb=" O PHE B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 590 Processing helix chain 'B' and resid 593 through 598 Processing helix chain 'B' and resid 599 through 603 removed outlier: 3.745A pdb=" N GLU B 603 " --> pdb=" O TYR B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 613 removed outlier: 3.982A pdb=" N CYS B 608 " --> pdb=" O ASP B 604 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N PHE B 609 " --> pdb=" O ARG B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 661 Processing helix chain 'B' and resid 662 through 668 Processing helix chain 'B' and resid 671 through 694 Processing helix chain 'B' and resid 694 through 710 removed outlier: 3.557A pdb=" N LEU B 710 " --> pdb=" O LEU B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 745 Processing helix chain 'B' and resid 750 through 787 removed outlier: 3.988A pdb=" N TYR B 754 " --> pdb=" O THR B 750 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR B 784 " --> pdb=" O ILE B 780 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY B 787 " --> pdb=" O ILE B 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 791 through 798 removed outlier: 3.698A pdb=" N PHE B 795 " --> pdb=" O THR B 791 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 822 removed outlier: 4.032A pdb=" N ALA B 807 " --> pdb=" O ASP B 803 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N THR B 808 " --> pdb=" O LEU B 804 " (cutoff:3.500A) Processing helix chain 'B' and resid 826 through 831 Processing helix chain 'B' and resid 831 through 853 Proline residue: B 840 - end of helix removed outlier: 3.808A pdb=" N LEU B 846 " --> pdb=" O TYR B 842 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASN B 847 " --> pdb=" O VAL B 843 " (cutoff:3.500A) Processing helix chain 'B' and resid 888 through 905 removed outlier: 3.662A pdb=" N ASP B 905 " --> pdb=" O GLU B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 917 through 946 removed outlier: 4.074A pdb=" N TYR B 921 " --> pdb=" O ASN B 917 " (cutoff:3.500A) Processing helix chain 'B' and resid 948 through 954 removed outlier: 4.213A pdb=" N ASN B 951 " --> pdb=" O GLY B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 955 through 1002 removed outlier: 4.239A pdb=" N ALA B 960 " --> pdb=" O ALA B 956 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N ASN B 961 " --> pdb=" O THR B 957 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER B 964 " --> pdb=" O ALA B 960 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASN B 965 " --> pdb=" O ASN B 961 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 239 through 240 removed outlier: 3.721A pdb=" N LYS B 874 " --> pdb=" O ASP B 882 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ARG A 391 " --> pdb=" O ALA B 873 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N LEU B 875 " --> pdb=" O ARG A 391 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 248 through 252 removed outlier: 8.104A pdb=" N PHE A 279 " --> pdb=" O THR A 405 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N THR A 405 " --> pdb=" O PHE A 279 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLN A 429 " --> pdb=" O ILE A 357 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N PHE A 541 " --> pdb=" O GLY A 493 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLY A 493 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N VAL A 488 " --> pdb=" O LEU A 621 " (cutoff:3.500A) removed outlier: 10.351A pdb=" N TYR A 623 " --> pdb=" O VAL A 488 " (cutoff:3.500A) removed outlier: 10.709A pdb=" N GLY A 490 " --> pdb=" O TYR A 623 " (cutoff:3.500A) removed outlier: 11.061A pdb=" N LYS A 625 " --> pdb=" O GLY A 490 " (cutoff:3.500A) removed outlier: 10.321A pdb=" N CYS A 492 " --> pdb=" O LYS A 625 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ALA A 627 " --> pdb=" O CYS A 492 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 409 through 413 removed outlier: 7.110A pdb=" N LYS A 419 " --> pdb=" O SER A 411 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 239 through 240 removed outlier: 3.720A pdb=" N LYS A 874 " --> pdb=" O ASP A 882 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 248 through 252 removed outlier: 8.104A pdb=" N PHE B 279 " --> pdb=" O THR B 405 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N THR B 405 " --> pdb=" O PHE B 279 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLN B 429 " --> pdb=" O ILE B 357 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N PHE B 541 " --> pdb=" O GLY B 493 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLY B 493 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N VAL B 488 " --> pdb=" O LEU B 621 " (cutoff:3.500A) removed outlier: 10.351A pdb=" N TYR B 623 " --> pdb=" O VAL B 488 " (cutoff:3.500A) removed outlier: 10.709A pdb=" N GLY B 490 " --> pdb=" O TYR B 623 " (cutoff:3.500A) removed outlier: 11.061A pdb=" N LYS B 625 " --> pdb=" O GLY B 490 " (cutoff:3.500A) removed outlier: 10.322A pdb=" N CYS B 492 " --> pdb=" O LYS B 625 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ALA B 627 " --> pdb=" O CYS B 492 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 409 through 413 removed outlier: 7.110A pdb=" N LYS B 419 " --> pdb=" O SER B 411 " (cutoff:3.500A) 759 hydrogen bonds defined for protein. 2169 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: 6.04 Time building geometry restraints manager: 3.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 12076 1.03 - 1.23: 46 1.23 - 1.42: 5676 1.42 - 1.61: 7446 1.61 - 1.81: 114 Bond restraints: 25358 Sorted by residual: bond pdb=" C4 UD1 A1206 " pdb=" O4 UD1 A1206 " ideal model delta sigma weight residual 1.217 1.393 -0.176 2.00e-02 2.50e+03 7.71e+01 bond pdb=" C4 UD1 B1206 " pdb=" O4 UD1 B1206 " ideal model delta sigma weight residual 1.217 1.392 -0.175 2.00e-02 2.50e+03 7.69e+01 bond pdb=" C1' UD1 B1206 " pdb=" O5' UD1 B1206 " ideal model delta sigma weight residual 1.392 1.553 -0.161 2.00e-02 2.50e+03 6.52e+01 bond pdb=" C1' UD1 A1206 " pdb=" O5' UD1 A1206 " ideal model delta sigma weight residual 1.392 1.553 -0.161 2.00e-02 2.50e+03 6.52e+01 bond pdb=" C7' UD1 A1206 " pdb=" N2' UD1 A1206 " ideal model delta sigma weight residual 1.347 1.500 -0.153 2.00e-02 2.50e+03 5.85e+01 ... (remaining 25353 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.33: 45027 3.33 - 6.65: 291 6.65 - 9.98: 24 9.98 - 13.30: 4 13.30 - 16.63: 12 Bond angle restraints: 45358 Sorted by residual: angle pdb=" O1' UD1 B1206 " pdb=" PB UD1 B1206 " pdb=" O3A UD1 B1206 " ideal model delta sigma weight residual 92.88 109.51 -16.63 3.00e+00 1.11e-01 3.07e+01 angle pdb=" O1' UD1 A1206 " pdb=" PB UD1 A1206 " pdb=" O3A UD1 A1206 " ideal model delta sigma weight residual 92.88 109.50 -16.62 3.00e+00 1.11e-01 3.07e+01 angle pdb=" O3A UD1 A1206 " pdb=" PA UD1 A1206 " pdb=" O5B UD1 A1206 " ideal model delta sigma weight residual 94.40 108.94 -14.54 3.00e+00 1.11e-01 2.35e+01 angle pdb=" O3A UD1 B1206 " pdb=" PA UD1 B1206 " pdb=" O5B UD1 B1206 " ideal model delta sigma weight residual 94.40 108.86 -14.46 3.00e+00 1.11e-01 2.32e+01 angle pdb=" O12 3PE A1201 " pdb=" P 3PE A1201 " pdb=" O14 3PE A1201 " ideal model delta sigma weight residual 123.79 109.40 14.39 3.00e+00 1.11e-01 2.30e+01 ... (remaining 45353 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 11541 17.93 - 35.85: 513 35.85 - 53.78: 175 53.78 - 71.71: 73 71.71 - 89.64: 8 Dihedral angle restraints: 12310 sinusoidal: 6470 harmonic: 5840 Sorted by residual: dihedral pdb=" O21 3PE A1201 " pdb=" C2 3PE A1201 " pdb=" C3 3PE A1201 " pdb=" O31 3PE A1201 " ideal model delta sinusoidal sigma weight residual 60.47 -29.17 89.64 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" O21 3PE B1201 " pdb=" C2 3PE B1201 " pdb=" C3 3PE B1201 " pdb=" O31 3PE B1201 " ideal model delta sinusoidal sigma weight residual 60.47 -29.14 89.61 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CA ASN A 798 " pdb=" CB ASN A 798 " pdb=" CG ASN A 798 " pdb=" OD1 ASN A 798 " ideal model delta sinusoidal sigma weight residual -90.00 -152.49 62.49 2 2.00e+01 2.50e-03 9.44e+00 ... (remaining 12307 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 1919 0.108 - 0.216: 59 0.216 - 0.324: 4 0.324 - 0.432: 0 0.432 - 0.540: 4 Chirality restraints: 1986 Sorted by residual: chirality pdb=" C1B UD1 B1206 " pdb=" C2B UD1 B1206 " pdb=" N1 UD1 B1206 " pdb=" O4B UD1 B1206 " both_signs ideal model delta sigma weight residual False 2.20 2.74 -0.54 2.00e-01 2.50e+01 7.29e+00 chirality pdb=" C1B UD1 A1206 " pdb=" C2B UD1 A1206 " pdb=" N1 UD1 A1206 " pdb=" O4B UD1 A1206 " both_signs ideal model delta sigma weight residual False 2.20 2.74 -0.54 2.00e-01 2.50e+01 7.23e+00 chirality pdb=" C2B UD1 A1206 " pdb=" C1B UD1 A1206 " pdb=" C3B UD1 A1206 " pdb=" O2' UD1 A1206 " both_signs ideal model delta sigma weight residual False -2.62 -3.06 0.45 2.00e-01 2.50e+01 4.97e+00 ... (remaining 1983 not shown) Planarity restraints: 3768 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN B 643 " 0.032 2.00e-02 2.50e+03 3.49e-02 1.83e+01 pdb=" CD GLN B 643 " 0.001 2.00e-02 2.50e+03 pdb=" OE1 GLN B 643 " -0.033 2.00e-02 2.50e+03 pdb=" NE2 GLN B 643 " 0.001 2.00e-02 2.50e+03 pdb="HE21 GLN B 643 " -0.051 2.00e-02 2.50e+03 pdb="HE22 GLN B 643 " 0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 643 " 0.032 2.00e-02 2.50e+03 3.48e-02 1.82e+01 pdb=" CD GLN A 643 " 0.001 2.00e-02 2.50e+03 pdb=" OE1 GLN A 643 " -0.033 2.00e-02 2.50e+03 pdb=" NE2 GLN A 643 " 0.001 2.00e-02 2.50e+03 pdb="HE21 GLN A 643 " -0.051 2.00e-02 2.50e+03 pdb="HE22 GLN A 643 " 0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 798 " 0.028 2.00e-02 2.50e+03 2.98e-02 1.33e+01 pdb=" CG ASN B 798 " -0.003 2.00e-02 2.50e+03 pdb=" OD1 ASN B 798 " -0.027 2.00e-02 2.50e+03 pdb=" ND2 ASN B 798 " 0.000 2.00e-02 2.50e+03 pdb="HD21 ASN B 798 " 0.044 2.00e-02 2.50e+03 pdb="HD22 ASN B 798 " -0.043 2.00e-02 2.50e+03 ... (remaining 3765 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.22: 1448 2.22 - 2.82: 51885 2.82 - 3.41: 64761 3.41 - 4.01: 86433 4.01 - 4.60: 137092 Nonbonded interactions: 341619 Sorted by model distance: nonbonded pdb=" OD1 ASN A 745 " pdb=" HG SER B 927 " model vdw 1.628 2.450 nonbonded pdb=" OE1 GLU B 341 " pdb=" HG SER B 353 " model vdw 1.632 2.450 nonbonded pdb=" OE1 GLU A 341 " pdb=" HG SER A 353 " model vdw 1.632 2.450 nonbonded pdb=" HG SER A 927 " pdb=" OD1 ASN B 745 " model vdw 1.644 2.450 nonbonded pdb=" H ASP B 142 " pdb=" OD2 ASP B 145 " model vdw 1.658 2.450 ... (remaining 341614 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.160 Extract box with map and model: 0.390 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 39.690 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.176 13258 Z= 0.424 Angle : 0.925 16.626 17952 Z= 0.460 Chirality : 0.050 0.540 1986 Planarity : 0.003 0.026 2220 Dihedral : 11.882 89.637 4878 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 1.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.31 % Allowed : 1.71 % Favored : 97.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.06 (0.21), residues: 1594 helix: 2.62 (0.17), residues: 854 sheet: 0.98 (0.46), residues: 146 loop : -0.44 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 926 TYR 0.009 0.001 TYR A 842 PHE 0.014 0.001 PHE A 984 TRP 0.010 0.001 TRP A 976 HIS 0.003 0.001 HIS A 670 Details of bonding type rmsd covalent geometry : bond 0.00783 (13258) covalent geometry : angle 0.92521 (17952) hydrogen bonds : bond 0.16572 ( 759) hydrogen bonds : angle 5.38547 ( 2169) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 137 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue ILE 553 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue LYS 748 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue THR 791 is missing expected H atoms. Skipping. Residue LEU 794 is missing expected H atoms. Skipping. Residue VAL 865 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue SER 884 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 889 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue ILE 1001 is missing expected H atoms. Skipping. Residue ILE 137 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue ILE 553 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue LYS 748 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue THR 791 is missing expected H atoms. Skipping. Residue LEU 794 is missing expected H atoms. Skipping. Residue VAL 865 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue SER 884 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 889 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue ILE 1001 is missing expected H atoms. Skipping. Evaluate side-chains 164 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 160 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 261 PHE cc_start: 0.7356 (m-10) cc_final: 0.7117 (m-10) REVERT: A 556 VAL cc_start: 0.9133 (m) cc_final: 0.8687 (p) REVERT: A 699 TYR cc_start: 0.8245 (OUTLIER) cc_final: 0.7312 (t80) REVERT: B 556 VAL cc_start: 0.9173 (m) cc_final: 0.8667 (p) REVERT: B 699 TYR cc_start: 0.8202 (OUTLIER) cc_final: 0.7244 (t80) outliers start: 4 outliers final: 2 residues processed: 164 average time/residue: 0.2587 time to fit residues: 62.4563 Evaluate side-chains 85 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 81 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 645 ARG Chi-restraints excluded: chain A residue 699 TYR Chi-restraints excluded: chain B residue 645 ARG Chi-restraints excluded: chain B residue 699 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.0070 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 5.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 438 ASN A 582 GLN A 598 ASN B 438 ASN B 582 GLN B 598 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.113427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.079616 restraints weight = 56277.536| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 2.52 r_work: 0.2833 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13258 Z= 0.108 Angle : 0.445 4.539 17952 Z= 0.242 Chirality : 0.038 0.142 1986 Planarity : 0.003 0.028 2220 Dihedral : 11.071 94.768 2164 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.78 % Allowed : 3.57 % Favored : 95.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.36 (0.21), residues: 1594 helix: 3.00 (0.17), residues: 848 sheet: 1.00 (0.43), residues: 144 loop : -0.45 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 391 TYR 0.012 0.001 TYR B 511 PHE 0.010 0.001 PHE B 640 TRP 0.011 0.001 TRP B 933 HIS 0.003 0.001 HIS A 303 Details of bonding type rmsd covalent geometry : bond 0.00218 (13258) covalent geometry : angle 0.44507 (17952) hydrogen bonds : bond 0.05371 ( 759) hydrogen bonds : angle 4.30951 ( 2169) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 137 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue ILE 553 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue LYS 748 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue THR 791 is missing expected H atoms. Skipping. Residue LEU 794 is missing expected H atoms. Skipping. Residue VAL 865 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue SER 884 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 889 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue ILE 1001 is missing expected H atoms. Skipping. Residue ILE 137 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue ILE 553 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue LYS 748 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue THR 791 is missing expected H atoms. Skipping. Residue LEU 794 is missing expected H atoms. Skipping. Residue VAL 865 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue SER 884 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 889 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue ILE 1001 is missing expected H atoms. Skipping. Evaluate side-chains 99 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 161 GLN cc_start: 0.8317 (mt0) cc_final: 0.8097 (pm20) REVERT: A 430 MET cc_start: 0.8637 (mmm) cc_final: 0.8307 (mmm) REVERT: A 645 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.7565 (tmt170) REVERT: A 699 TYR cc_start: 0.8594 (OUTLIER) cc_final: 0.7366 (t80) REVERT: B 430 MET cc_start: 0.8613 (mmm) cc_final: 0.8277 (mmm) REVERT: B 645 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7708 (tmt170) REVERT: B 699 TYR cc_start: 0.8544 (OUTLIER) cc_final: 0.7313 (t80) outliers start: 10 outliers final: 6 residues processed: 95 average time/residue: 0.2198 time to fit residues: 32.6606 Evaluate side-chains 90 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 438 ASN Chi-restraints excluded: chain A residue 645 ARG Chi-restraints excluded: chain A residue 699 TYR Chi-restraints excluded: chain A residue 820 PHE Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 438 ASN Chi-restraints excluded: chain B residue 645 ARG Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain B residue 820 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 75 optimal weight: 9.9990 chunk 58 optimal weight: 10.0000 chunk 126 optimal weight: 0.8980 chunk 69 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 6 optimal weight: 8.9990 chunk 83 optimal weight: 9.9990 chunk 142 optimal weight: 5.9990 chunk 117 optimal weight: 9.9990 chunk 78 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.106168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.072157 restraints weight = 57606.908| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 2.42 r_work: 0.2700 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2564 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 13258 Z= 0.272 Angle : 0.527 4.738 17952 Z= 0.293 Chirality : 0.042 0.145 1986 Planarity : 0.003 0.038 2220 Dihedral : 11.581 91.197 2164 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.26 % Favored : 96.49 % Rotamer: Outliers : 0.47 % Allowed : 4.11 % Favored : 95.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.94 (0.21), residues: 1594 helix: 2.54 (0.17), residues: 854 sheet: 0.86 (0.44), residues: 148 loop : -0.50 (0.24), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 446 TYR 0.012 0.001 TYR A 842 PHE 0.019 0.002 PHE A 984 TRP 0.013 0.002 TRP A 933 HIS 0.003 0.001 HIS B 303 Details of bonding type rmsd covalent geometry : bond 0.00639 (13258) covalent geometry : angle 0.52714 (17952) hydrogen bonds : bond 0.06721 ( 759) hydrogen bonds : angle 4.41055 ( 2169) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 137 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue ILE 553 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue LYS 748 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue THR 791 is missing expected H atoms. Skipping. Residue LEU 794 is missing expected H atoms. Skipping. Residue VAL 865 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue SER 884 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 889 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue ILE 1001 is missing expected H atoms. Skipping. Residue ILE 137 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue ILE 553 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue LYS 748 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue THR 791 is missing expected H atoms. Skipping. Residue LEU 794 is missing expected H atoms. Skipping. Residue VAL 865 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue SER 884 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 889 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue ILE 1001 is missing expected H atoms. Skipping. Evaluate side-chains 90 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 84 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 GLN cc_start: 0.8394 (mt0) cc_final: 0.8183 (pm20) REVERT: A 309 GLN cc_start: 0.8633 (pm20) cc_final: 0.8346 (mp10) REVERT: A 430 MET cc_start: 0.8782 (mmm) cc_final: 0.8463 (mmm) REVERT: A 645 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.8048 (tmt170) REVERT: A 699 TYR cc_start: 0.9063 (OUTLIER) cc_final: 0.7910 (t80) REVERT: B 309 GLN cc_start: 0.8628 (pm20) cc_final: 0.8347 (mp10) REVERT: B 430 MET cc_start: 0.8760 (mmm) cc_final: 0.8421 (mmm) REVERT: B 645 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.8034 (tmt170) REVERT: B 699 TYR cc_start: 0.9047 (OUTLIER) cc_final: 0.7918 (t80) REVERT: B 882 ASP cc_start: 0.7666 (m-30) cc_final: 0.6586 (p0) outliers start: 6 outliers final: 1 residues processed: 90 average time/residue: 0.2957 time to fit residues: 37.9225 Evaluate side-chains 77 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 645 ARG Chi-restraints excluded: chain A residue 699 TYR Chi-restraints excluded: chain A residue 989 CYS Chi-restraints excluded: chain B residue 645 ARG Chi-restraints excluded: chain B residue 699 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 51 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 chunk 132 optimal weight: 2.9990 chunk 82 optimal weight: 9.9990 chunk 128 optimal weight: 0.9990 chunk 2 optimal weight: 10.0000 chunk 119 optimal weight: 2.9990 chunk 157 optimal weight: 0.5980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 438 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.113085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.079811 restraints weight = 55737.735| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.41 r_work: 0.2841 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13258 Z= 0.134 Angle : 0.428 4.560 17952 Z= 0.235 Chirality : 0.038 0.140 1986 Planarity : 0.003 0.032 2220 Dihedral : 10.899 90.874 2164 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.25 % Allowed : 2.45 % Favored : 97.30 % Rotamer: Outliers : 0.54 % Allowed : 4.74 % Favored : 94.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.07 (0.21), residues: 1594 helix: 2.81 (0.17), residues: 846 sheet: 0.78 (0.43), residues: 148 loop : -0.65 (0.23), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 281 TYR 0.010 0.001 TYR B 511 PHE 0.011 0.001 PHE B 984 TRP 0.010 0.001 TRP B 976 HIS 0.002 0.001 HIS A 679 Details of bonding type rmsd covalent geometry : bond 0.00305 (13258) covalent geometry : angle 0.42766 (17952) hydrogen bonds : bond 0.05252 ( 759) hydrogen bonds : angle 4.13378 ( 2169) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 137 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue ILE 553 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue LYS 748 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue THR 791 is missing expected H atoms. Skipping. Residue LEU 794 is missing expected H atoms. Skipping. Residue VAL 865 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue SER 884 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 889 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue ILE 1001 is missing expected H atoms. Skipping. Residue ILE 137 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue ILE 553 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue LYS 748 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue THR 791 is missing expected H atoms. Skipping. Residue LEU 794 is missing expected H atoms. Skipping. Residue VAL 865 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue SER 884 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 889 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue ILE 1001 is missing expected H atoms. Skipping. Evaluate side-chains 88 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 81 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 GLN cc_start: 0.8375 (mt0) cc_final: 0.8160 (pm20) REVERT: A 645 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.8074 (tmt170) REVERT: A 699 TYR cc_start: 0.9023 (OUTLIER) cc_final: 0.8040 (t80) REVERT: A 882 ASP cc_start: 0.7749 (m-30) cc_final: 0.6676 (p0) REVERT: B 309 GLN cc_start: 0.8633 (pm20) cc_final: 0.8402 (mp10) REVERT: B 430 MET cc_start: 0.8776 (mmm) cc_final: 0.8465 (mmm) REVERT: B 645 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.8089 (tmt170) REVERT: B 699 TYR cc_start: 0.9020 (OUTLIER) cc_final: 0.8081 (t80) REVERT: B 882 ASP cc_start: 0.7685 (m-30) cc_final: 0.6615 (p0) outliers start: 7 outliers final: 1 residues processed: 87 average time/residue: 0.2287 time to fit residues: 30.6606 Evaluate side-chains 77 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 645 ARG Chi-restraints excluded: chain A residue 699 TYR Chi-restraints excluded: chain B residue 438 ASN Chi-restraints excluded: chain B residue 645 ARG Chi-restraints excluded: chain B residue 699 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 24 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 chunk 107 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 2 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 chunk 115 optimal weight: 0.1980 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.111651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.076852 restraints weight = 55898.438| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 2.53 r_work: 0.2822 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 13258 Z= 0.160 Angle : 0.433 4.579 17952 Z= 0.238 Chirality : 0.038 0.141 1986 Planarity : 0.003 0.034 2220 Dihedral : 10.734 88.465 2164 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 1.64 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.01 % Favored : 96.74 % Rotamer: Outliers : 0.78 % Allowed : 4.50 % Favored : 94.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.04 (0.21), residues: 1594 helix: 2.83 (0.17), residues: 846 sheet: 0.82 (0.43), residues: 148 loop : -0.74 (0.23), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 446 TYR 0.011 0.001 TYR B 511 PHE 0.013 0.001 PHE A 984 TRP 0.009 0.001 TRP B 976 HIS 0.002 0.001 HIS A 679 Details of bonding type rmsd covalent geometry : bond 0.00371 (13258) covalent geometry : angle 0.43252 (17952) hydrogen bonds : bond 0.05405 ( 759) hydrogen bonds : angle 4.10166 ( 2169) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 137 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue ILE 553 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue LYS 748 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue THR 791 is missing expected H atoms. Skipping. Residue LEU 794 is missing expected H atoms. Skipping. Residue VAL 865 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue SER 884 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 889 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue ILE 1001 is missing expected H atoms. Skipping. Residue ILE 137 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue ILE 553 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue LYS 748 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue THR 791 is missing expected H atoms. Skipping. Residue LEU 794 is missing expected H atoms. Skipping. Residue VAL 865 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue SER 884 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 889 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue ILE 1001 is missing expected H atoms. Skipping. Evaluate side-chains 83 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 645 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.8139 (tmt170) REVERT: A 699 TYR cc_start: 0.9055 (OUTLIER) cc_final: 0.8085 (t80) REVERT: A 882 ASP cc_start: 0.7784 (m-30) cc_final: 0.6524 (p0) REVERT: B 430 MET cc_start: 0.8768 (mmm) cc_final: 0.8460 (mmm) REVERT: B 645 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.8143 (tmt170) REVERT: B 699 TYR cc_start: 0.9045 (OUTLIER) cc_final: 0.8088 (t80) outliers start: 10 outliers final: 2 residues processed: 81 average time/residue: 0.2243 time to fit residues: 28.5160 Evaluate side-chains 72 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 645 ARG Chi-restraints excluded: chain A residue 699 TYR Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain B residue 645 ARG Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain B residue 715 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 132 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 118 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 152 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 chunk 65 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.111087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.076339 restraints weight = 56104.096| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 2.53 r_work: 0.2811 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 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 : 0.004 0.039 13258 Z= 0.156 Angle : 0.432 5.919 17952 Z= 0.237 Chirality : 0.038 0.141 1986 Planarity : 0.003 0.031 2220 Dihedral : 10.677 88.099 2164 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.01 % Favored : 96.74 % Rotamer: Outliers : 0.62 % Allowed : 4.27 % Favored : 95.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.05 (0.21), residues: 1594 helix: 2.86 (0.17), residues: 846 sheet: 0.86 (0.44), residues: 148 loop : -0.79 (0.23), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 446 TYR 0.011 0.001 TYR B 511 PHE 0.013 0.001 PHE B 984 TRP 0.009 0.001 TRP B 976 HIS 0.002 0.001 HIS A 679 Details of bonding type rmsd covalent geometry : bond 0.00361 (13258) covalent geometry : angle 0.43242 (17952) hydrogen bonds : bond 0.05284 ( 759) hydrogen bonds : angle 4.05663 ( 2169) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 137 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue ILE 553 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue LYS 748 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue THR 791 is missing expected H atoms. Skipping. Residue LEU 794 is missing expected H atoms. Skipping. Residue VAL 865 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue SER 884 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 889 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue ILE 1001 is missing expected H atoms. Skipping. Residue ILE 137 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue ILE 553 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue LYS 748 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue THR 791 is missing expected H atoms. Skipping. Residue LEU 794 is missing expected H atoms. Skipping. Residue VAL 865 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue SER 884 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 889 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue ILE 1001 is missing expected H atoms. Skipping. Evaluate side-chains 76 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 494 GLU cc_start: 0.8957 (OUTLIER) cc_final: 0.8016 (tt0) REVERT: A 699 TYR cc_start: 0.9034 (OUTLIER) cc_final: 0.8079 (t80) REVERT: A 882 ASP cc_start: 0.7837 (m-30) cc_final: 0.6612 (p0) REVERT: B 430 MET cc_start: 0.8778 (mmm) cc_final: 0.8474 (mmm) REVERT: B 494 GLU cc_start: 0.8979 (OUTLIER) cc_final: 0.8045 (tt0) REVERT: B 699 TYR cc_start: 0.9032 (OUTLIER) cc_final: 0.8086 (t80) outliers start: 8 outliers final: 2 residues processed: 74 average time/residue: 0.1779 time to fit residues: 21.9454 Evaluate side-chains 71 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 699 TYR Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain B residue 715 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 119 optimal weight: 4.9990 chunk 141 optimal weight: 4.9990 chunk 84 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 81 optimal weight: 7.9990 chunk 78 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.108127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.073256 restraints weight = 56245.707| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 2.52 r_work: 0.2740 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2604 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 13258 Z= 0.252 Angle : 0.492 4.790 17952 Z= 0.273 Chirality : 0.041 0.143 1986 Planarity : 0.003 0.035 2220 Dihedral : 11.277 90.199 2156 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.51 % Favored : 96.24 % Rotamer: Outliers : 0.54 % Allowed : 4.97 % Favored : 94.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.75 (0.21), residues: 1594 helix: 2.56 (0.17), residues: 844 sheet: 0.68 (0.43), residues: 148 loop : -0.82 (0.23), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 446 TYR 0.012 0.001 TYR B 511 PHE 0.019 0.001 PHE A 984 TRP 0.011 0.002 TRP A 693 HIS 0.004 0.001 HIS B 400 Details of bonding type rmsd covalent geometry : bond 0.00601 (13258) covalent geometry : angle 0.49201 (17952) hydrogen bonds : bond 0.06377 ( 759) hydrogen bonds : angle 4.28767 ( 2169) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 137 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue ILE 553 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue LYS 748 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue THR 791 is missing expected H atoms. Skipping. Residue LEU 794 is missing expected H atoms. Skipping. Residue VAL 865 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue SER 884 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 889 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue ILE 1001 is missing expected H atoms. Skipping. Residue ILE 137 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue ILE 553 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue LYS 748 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue THR 791 is missing expected H atoms. Skipping. Residue LEU 794 is missing expected H atoms. Skipping. Residue VAL 865 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue SER 884 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 889 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue ILE 1001 is missing expected H atoms. Skipping. Evaluate side-chains 69 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 494 GLU cc_start: 0.8927 (OUTLIER) cc_final: 0.8075 (tt0) REVERT: A 699 TYR cc_start: 0.9083 (OUTLIER) cc_final: 0.8012 (t80) REVERT: B 494 GLU cc_start: 0.8944 (OUTLIER) cc_final: 0.8101 (tt0) REVERT: B 699 TYR cc_start: 0.9084 (OUTLIER) cc_final: 0.8077 (t80) outliers start: 7 outliers final: 2 residues processed: 67 average time/residue: 0.1917 time to fit residues: 21.6125 Evaluate side-chains 68 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 699 TYR Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain B residue 715 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 56 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 142 optimal weight: 0.9990 chunk 83 optimal weight: 10.0000 chunk 42 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 133 optimal weight: 0.5980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.110485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.075737 restraints weight = 55792.540| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 2.53 r_work: 0.2796 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13258 Z= 0.121 Angle : 0.417 4.533 17952 Z= 0.230 Chirality : 0.038 0.140 1986 Planarity : 0.003 0.032 2220 Dihedral : 10.834 90.776 2156 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.25 % Allowed : 2.82 % Favored : 96.93 % Rotamer: Outliers : 0.39 % Allowed : 5.12 % Favored : 94.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.00 (0.21), residues: 1594 helix: 2.81 (0.18), residues: 844 sheet: 0.68 (0.43), residues: 148 loop : -0.73 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 446 TYR 0.010 0.001 TYR B 511 PHE 0.012 0.001 PHE A 984 TRP 0.010 0.001 TRP B 976 HIS 0.002 0.001 HIS B 679 Details of bonding type rmsd covalent geometry : bond 0.00269 (13258) covalent geometry : angle 0.41718 (17952) hydrogen bonds : bond 0.05197 ( 759) hydrogen bonds : angle 4.07936 ( 2169) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 137 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue ILE 553 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue LYS 748 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue THR 791 is missing expected H atoms. Skipping. Residue LEU 794 is missing expected H atoms. Skipping. Residue VAL 865 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue SER 884 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 889 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue ILE 1001 is missing expected H atoms. Skipping. Residue ILE 137 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue ILE 553 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue LYS 748 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue THR 791 is missing expected H atoms. Skipping. Residue LEU 794 is missing expected H atoms. Skipping. Residue VAL 865 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue SER 884 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 889 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue ILE 1001 is missing expected H atoms. Skipping. Evaluate side-chains 69 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 699 TYR cc_start: 0.9037 (OUTLIER) cc_final: 0.8056 (t80) REVERT: B 699 TYR cc_start: 0.9039 (OUTLIER) cc_final: 0.8066 (t80) outliers start: 5 outliers final: 2 residues processed: 67 average time/residue: 0.1787 time to fit residues: 20.3915 Evaluate side-chains 64 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 60 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 699 TYR Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain B residue 715 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 66 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 chunk 101 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 chunk 88 optimal weight: 3.9990 chunk 156 optimal weight: 5.9990 chunk 115 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.109469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.074683 restraints weight = 56181.548| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 2.53 r_work: 0.2771 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2632 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.3704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 13258 Z= 0.166 Angle : 0.433 4.603 17952 Z= 0.239 Chirality : 0.039 0.140 1986 Planarity : 0.003 0.034 2220 Dihedral : 10.896 90.027 2156 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.58 % Favored : 96.17 % Rotamer: Outliers : 0.47 % Allowed : 5.05 % Favored : 94.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.95 (0.21), residues: 1594 helix: 2.76 (0.17), residues: 844 sheet: 0.54 (0.42), residues: 148 loop : -0.71 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 446 TYR 0.011 0.001 TYR B 511 PHE 0.014 0.001 PHE A 984 TRP 0.009 0.001 TRP A 976 HIS 0.002 0.001 HIS A 400 Details of bonding type rmsd covalent geometry : bond 0.00388 (13258) covalent geometry : angle 0.43280 (17952) hydrogen bonds : bond 0.05497 ( 759) hydrogen bonds : angle 4.10315 ( 2169) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 137 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue ILE 553 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue LYS 748 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue THR 791 is missing expected H atoms. Skipping. Residue LEU 794 is missing expected H atoms. Skipping. Residue VAL 865 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue SER 884 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 889 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue ILE 1001 is missing expected H atoms. Skipping. Residue ILE 137 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue ILE 553 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue LYS 748 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue THR 791 is missing expected H atoms. Skipping. Residue LEU 794 is missing expected H atoms. Skipping. Residue VAL 865 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue SER 884 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 889 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue ILE 1001 is missing expected H atoms. Skipping. Evaluate side-chains 72 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 494 GLU cc_start: 0.8898 (OUTLIER) cc_final: 0.8043 (tt0) REVERT: A 699 TYR cc_start: 0.9056 (OUTLIER) cc_final: 0.8116 (t80) REVERT: A 882 ASP cc_start: 0.7668 (m-30) cc_final: 0.6448 (p0) REVERT: B 494 GLU cc_start: 0.8900 (OUTLIER) cc_final: 0.8048 (tt0) REVERT: B 699 TYR cc_start: 0.9058 (OUTLIER) cc_final: 0.8124 (t80) outliers start: 6 outliers final: 2 residues processed: 70 average time/residue: 0.2052 time to fit residues: 23.3744 Evaluate side-chains 67 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 699 TYR Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain B residue 715 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 104 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 136 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 132 optimal weight: 0.6980 chunk 68 optimal weight: 9.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 ASN B 336 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.111176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.076569 restraints weight = 55743.531| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 2.52 r_work: 0.2814 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13258 Z= 0.105 Angle : 0.401 4.498 17952 Z= 0.219 Chirality : 0.038 0.137 1986 Planarity : 0.003 0.032 2220 Dihedral : 10.508 88.449 2156 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.25 % Allowed : 2.63 % Favored : 97.11 % Rotamer: Outliers : 0.47 % Allowed : 5.12 % Favored : 94.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.15 (0.21), residues: 1594 helix: 2.95 (0.18), residues: 844 sheet: 0.64 (0.43), residues: 148 loop : -0.66 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 646 TYR 0.008 0.001 TYR B 511 PHE 0.010 0.001 PHE A 984 TRP 0.010 0.001 TRP B 976 HIS 0.001 0.000 HIS B 679 Details of bonding type rmsd covalent geometry : bond 0.00227 (13258) covalent geometry : angle 0.40067 (17952) hydrogen bonds : bond 0.04756 ( 759) hydrogen bonds : angle 3.95743 ( 2169) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 137 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue ILE 553 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue LYS 748 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue THR 791 is missing expected H atoms. Skipping. Residue LEU 794 is missing expected H atoms. Skipping. Residue VAL 865 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue SER 884 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 889 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue ILE 1001 is missing expected H atoms. Skipping. Residue ILE 137 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue ILE 553 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue LYS 748 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue THR 791 is missing expected H atoms. Skipping. Residue LEU 794 is missing expected H atoms. Skipping. Residue VAL 865 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue SER 884 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 889 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue ILE 1001 is missing expected H atoms. Skipping. Evaluate side-chains 70 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 494 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.8011 (tt0) REVERT: A 699 TYR cc_start: 0.9006 (OUTLIER) cc_final: 0.8129 (t80) REVERT: A 882 ASP cc_start: 0.7650 (m-30) cc_final: 0.6467 (p0) REVERT: B 494 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.8001 (tt0) REVERT: B 699 TYR cc_start: 0.9004 (OUTLIER) cc_final: 0.8130 (t80) outliers start: 6 outliers final: 2 residues processed: 68 average time/residue: 0.1939 time to fit residues: 22.2218 Evaluate side-chains 69 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 699 TYR Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain B residue 715 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 61 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 106 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 125 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.111327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.076618 restraints weight = 55909.530| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 2.54 r_work: 0.2811 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2673 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.3780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 13258 Z= 0.115 Angle : 0.401 4.483 17952 Z= 0.219 Chirality : 0.038 0.139 1986 Planarity : 0.003 0.032 2220 Dihedral : 10.322 86.573 2156 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.51 % Favored : 96.24 % Rotamer: Outliers : 0.47 % Allowed : 5.05 % Favored : 94.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.17 (0.21), residues: 1594 helix: 2.99 (0.18), residues: 846 sheet: 0.60 (0.43), residues: 148 loop : -0.70 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 446 TYR 0.009 0.001 TYR B 511 PHE 0.010 0.001 PHE A 984 TRP 0.010 0.001 TRP B 976 HIS 0.002 0.000 HIS B 679 Details of bonding type rmsd covalent geometry : bond 0.00257 (13258) covalent geometry : angle 0.40085 (17952) hydrogen bonds : bond 0.04723 ( 759) hydrogen bonds : angle 3.91188 ( 2169) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5940.21 seconds wall clock time: 101 minutes 26.63 seconds (6086.63 seconds total)