Starting phenix.real_space_refine on Sun Jun 22 10:17:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7stm_25433/06_2025/7stm_25433_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7stm_25433/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7stm_25433/06_2025/7stm_25433.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7stm_25433/06_2025/7stm_25433.map" model { file = "/net/cci-nas-00/data/ceres_data/7stm_25433/06_2025/7stm_25433_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7stm_25433/06_2025/7stm_25433_trim.cif" } resolution = 3.02 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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, 'GLU:plan': 11, 'ARG:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 11} 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: 41.60, per 1000 atoms: 1.66 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: 7.56 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 1.97 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: 10.45 Time building geometry restraints manager: 9.01 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: 0.07 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: 0.600 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: 0.430 Extract box with map and model: 0.990 Check model and map are aligned: 0.170 Set scattering table: 0.260 Process input model: 86.420 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.360 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.010 0.001 TRP A 976 HIS 0.003 0.001 HIS A 670 PHE 0.014 0.001 PHE A 984 TYR 0.009 0.001 TYR A 842 ARG 0.003 0.000 ARG B 926 Details of bonding type rmsd hydrogen bonds : bond 0.16572 ( 759) hydrogen bonds : angle 5.38547 ( 2169) covalent geometry : bond 0.00783 (13258) covalent geometry : angle 0.92521 (17952) *********************** 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 : 2.143 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: 0.8688 (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 645 ARG cc_start: 0.8384 (OUTLIER) cc_final: 0.8164 (ttp80) REVERT: B 699 TYR cc_start: 0.8202 (OUTLIER) cc_final: 0.7242 (t80) outliers start: 4 outliers final: 1 residues processed: 164 average time/residue: 0.5279 time to fit residues: 127.1402 Evaluate side-chains 83 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 79 time to evaluate : 1.860 ------------------------------------------------------------------------------- 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 135 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 chunk 67 optimal weight: 20.0000 chunk 41 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 chunk 64 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 145 optimal weight: 0.6980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 582 GLN A 598 ASN B 582 GLN B 598 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.111141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.077236 restraints weight = 56232.580| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 2.50 r_work: 0.2792 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1624 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= 0.135 Angle : 0.474 4.591 17952 Z= 0.257 Chirality : 0.039 0.145 1986 Planarity : 0.003 0.029 2220 Dihedral : 11.102 96.012 2164 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 1.56 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.51 % Favored : 97.37 % Rotamer: Outliers : 0.47 % Allowed : 3.65 % Favored : 95.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.21), residues: 1594 helix: 2.92 (0.17), residues: 844 sheet: 0.93 (0.43), residues: 144 loop : -0.37 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 933 HIS 0.004 0.001 HIS B 303 PHE 0.011 0.001 PHE B 984 TYR 0.013 0.001 TYR B 511 ARG 0.002 0.000 ARG A 644 Details of bonding type rmsd hydrogen bonds : bond 0.05449 ( 759) hydrogen bonds : angle 4.28848 ( 2169) covalent geometry : bond 0.00298 (13258) covalent geometry : angle 0.47374 (17952) *********************** 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 94 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 1.884 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 430 MET cc_start: 0.8656 (mmm) cc_final: 0.8309 (mmm) REVERT: A 645 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.7685 (tmt170) REVERT: A 699 TYR cc_start: 0.8722 (OUTLIER) cc_final: 0.7582 (t80) REVERT: B 430 MET cc_start: 0.8650 (mmm) cc_final: 0.8283 (mmm) REVERT: B 645 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.7701 (tmt170) REVERT: B 699 TYR cc_start: 0.8665 (OUTLIER) cc_final: 0.7534 (t80) outliers start: 6 outliers final: 2 residues processed: 92 average time/residue: 0.5348 time to fit residues: 74.3666 Evaluate side-chains 82 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 2.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 645 ARG Chi-restraints excluded: chain A residue 699 TYR Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 645 ARG Chi-restraints excluded: chain B residue 699 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 96 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 151 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 117 optimal weight: 9.9990 chunk 159 optimal weight: 0.0050 chunk 91 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 overall best weight: 1.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.110203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.076758 restraints weight = 56746.735| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 2.42 r_work: 0.2790 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13258 Z= 0.129 Angle : 0.417 4.525 17952 Z= 0.228 Chirality : 0.038 0.140 1986 Planarity : 0.003 0.031 2220 Dihedral : 10.725 91.107 2164 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.25 % Allowed : 2.76 % Favored : 96.99 % Rotamer: Outliers : 0.78 % Allowed : 3.26 % Favored : 95.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.21), residues: 1594 helix: 3.02 (0.17), residues: 846 sheet: 0.91 (0.43), residues: 144 loop : -0.43 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 976 HIS 0.002 0.001 HIS A 679 PHE 0.015 0.001 PHE A 261 TYR 0.008 0.001 TYR A 842 ARG 0.003 0.000 ARG B 446 Details of bonding type rmsd hydrogen bonds : bond 0.05203 ( 759) hydrogen bonds : angle 4.03801 ( 2169) covalent geometry : bond 0.00291 (13258) covalent geometry : angle 0.41733 (17952) *********************** 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 91 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 1.936 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 309 GLN cc_start: 0.8668 (pm20) cc_final: 0.8264 (mp10) REVERT: A 430 MET cc_start: 0.8692 (mmm) cc_final: 0.8369 (mmm) REVERT: A 645 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7931 (tmt170) REVERT: A 699 TYR cc_start: 0.8894 (OUTLIER) cc_final: 0.7880 (t80) REVERT: B 309 GLN cc_start: 0.8690 (pm20) cc_final: 0.8344 (mp10) REVERT: B 430 MET cc_start: 0.8708 (mmm) cc_final: 0.8378 (mmm) REVERT: B 645 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.8017 (tmt170) REVERT: B 699 TYR cc_start: 0.8880 (OUTLIER) cc_final: 0.7902 (t80) outliers start: 10 outliers final: 6 residues processed: 87 average time/residue: 0.4976 time to fit residues: 65.8625 Evaluate side-chains 80 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 1.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 LEU 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 A residue 989 CYS Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 645 ARG Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain B residue 820 PHE Chi-restraints excluded: chain B residue 989 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 105 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 75 optimal weight: 10.0000 chunk 79 optimal weight: 0.1980 chunk 36 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 92 optimal weight: 4.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 336 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.107805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.074434 restraints weight = 57474.719| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 2.40 r_work: 0.2746 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2609 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2739 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= 0.146 Angle : 0.437 4.527 17952 Z= 0.237 Chirality : 0.039 0.142 1986 Planarity : 0.003 0.031 2220 Dihedral : 10.536 89.982 2164 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.25 % Allowed : 2.38 % Favored : 97.37 % Rotamer: Outliers : 0.31 % Allowed : 4.27 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.21), residues: 1594 helix: 2.94 (0.17), residues: 846 sheet: 0.72 (0.43), residues: 148 loop : -0.57 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 976 HIS 0.003 0.001 HIS A 303 PHE 0.013 0.001 PHE B 984 TYR 0.012 0.001 TYR A 511 ARG 0.003 0.000 ARG B 446 Details of bonding type rmsd hydrogen bonds : bond 0.05132 ( 759) hydrogen bonds : angle 4.00657 ( 2169) covalent geometry : bond 0.00335 (13258) covalent geometry : angle 0.43651 (17952) *********************** 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 83 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 79 time to evaluate : 1.907 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 309 GLN cc_start: 0.8686 (pm20) cc_final: 0.8456 (mp10) REVERT: A 430 MET cc_start: 0.8743 (mmm) cc_final: 0.8401 (mmm) REVERT: A 699 TYR cc_start: 0.8994 (OUTLIER) cc_final: 0.7978 (t80) REVERT: A 882 ASP cc_start: 0.7708 (m-30) cc_final: 0.6633 (p0) REVERT: B 309 GLN cc_start: 0.8710 (pm20) cc_final: 0.8414 (mp10) REVERT: B 430 MET cc_start: 0.8738 (mmm) cc_final: 0.8376 (mmm) REVERT: B 699 TYR cc_start: 0.8989 (OUTLIER) cc_final: 0.7975 (t80) REVERT: B 882 ASP cc_start: 0.7669 (m-30) cc_final: 0.6584 (p0) outliers start: 4 outliers final: 0 residues processed: 83 average time/residue: 0.5519 time to fit residues: 68.2602 Evaluate side-chains 71 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 69 time to evaluate : 2.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 699 TYR 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 144 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 115 optimal weight: 0.0570 chunk 107 optimal weight: 4.9990 chunk 80 optimal weight: 20.0000 chunk 116 optimal weight: 3.9990 chunk 89 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 overall best weight: 2.4106 ------------------------------------------------------------------------------- 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 = 0.3540 r_free = 0.3540 target = 0.111473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.076690 restraints weight = 56574.401| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 2.54 r_work: 0.2812 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2673 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 13258 Z= 0.167 Angle : 0.438 4.623 17952 Z= 0.243 Chirality : 0.039 0.140 1986 Planarity : 0.003 0.032 2220 Dihedral : 10.460 85.844 2156 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.25 % Allowed : 2.95 % Favored : 96.80 % Rotamer: Outliers : 0.54 % Allowed : 4.27 % Favored : 95.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.21), residues: 1594 helix: 2.91 (0.17), residues: 844 sheet: 0.62 (0.43), residues: 148 loop : -0.58 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 693 HIS 0.003 0.001 HIS A 400 PHE 0.014 0.001 PHE A 984 TYR 0.010 0.001 TYR B 511 ARG 0.004 0.001 ARG B 281 Details of bonding type rmsd hydrogen bonds : bond 0.05481 ( 759) hydrogen bonds : angle 4.06581 ( 2169) covalent geometry : bond 0.00385 (13258) covalent geometry : angle 0.43796 (17952) *********************** 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 79 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 2.123 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 430 MET cc_start: 0.8833 (mmm) cc_final: 0.8534 (mmm) REVERT: A 699 TYR cc_start: 0.9052 (OUTLIER) cc_final: 0.8053 (t80) REVERT: A 882 ASP cc_start: 0.7854 (m-30) cc_final: 0.6622 (p0) REVERT: B 430 MET cc_start: 0.8815 (mmm) cc_final: 0.8518 (mmm) REVERT: B 699 TYR cc_start: 0.9050 (OUTLIER) cc_final: 0.8069 (t80) outliers start: 7 outliers final: 1 residues processed: 78 average time/residue: 0.4588 time to fit residues: 56.4928 Evaluate side-chains 67 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 64 time to evaluate : 2.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 699 TYR Chi-restraints excluded: chain B residue 699 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 53 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 89 optimal weight: 0.0020 chunk 60 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 overall best weight: 1.9996 ------------------------------------------------------------------------------- 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 = 0.110720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.077325 restraints weight = 56078.345| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 2.43 r_work: 0.2822 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13258 Z= 0.143 Angle : 0.423 5.170 17952 Z= 0.232 Chirality : 0.038 0.139 1986 Planarity : 0.003 0.031 2220 Dihedral : 10.357 86.514 2156 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.25 % Allowed : 2.45 % Favored : 97.30 % Rotamer: Outliers : 0.54 % Allowed : 4.19 % Favored : 95.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.21), residues: 1594 helix: 2.93 (0.18), residues: 846 sheet: 0.62 (0.43), residues: 148 loop : -0.64 (0.23), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 976 HIS 0.002 0.001 HIS A 679 PHE 0.012 0.001 PHE B 984 TYR 0.011 0.001 TYR B 511 ARG 0.005 0.000 ARG A 281 Details of bonding type rmsd hydrogen bonds : bond 0.05143 ( 759) hydrogen bonds : angle 3.99096 ( 2169) covalent geometry : bond 0.00329 (13258) covalent geometry : angle 0.42296 (17952) *********************** 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 71 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 2.048 Fit side-chains revert: symmetry clash REVERT: A 430 MET cc_start: 0.8798 (mmm) cc_final: 0.8493 (mmm) REVERT: A 494 GLU cc_start: 0.8966 (OUTLIER) cc_final: 0.8070 (tt0) REVERT: A 699 TYR cc_start: 0.9028 (OUTLIER) cc_final: 0.8042 (t80) REVERT: A 882 ASP cc_start: 0.7848 (m-30) cc_final: 0.6613 (p0) REVERT: B 430 MET cc_start: 0.8791 (mmm) cc_final: 0.8480 (mmm) REVERT: B 494 GLU cc_start: 0.8971 (OUTLIER) cc_final: 0.8028 (tt0) REVERT: B 699 TYR cc_start: 0.9027 (OUTLIER) cc_final: 0.8043 (t80) outliers start: 7 outliers final: 1 residues processed: 70 average time/residue: 0.4144 time to fit residues: 48.2421 Evaluate side-chains 67 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 2.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 699 TYR Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 699 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 154 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 159 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 138 optimal weight: 0.0010 chunk 29 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 overall best weight: 2.1994 ------------------------------------------------------------------------------- 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 = 0.3526 r_free = 0.3526 target = 0.110894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.076028 restraints weight = 56061.767| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 2.54 r_work: 0.2775 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2636 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.3444 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= 0.155 Angle : 0.420 4.584 17952 Z= 0.232 Chirality : 0.038 0.140 1986 Planarity : 0.003 0.031 2220 Dihedral : 10.434 86.687 2156 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.26 % Favored : 96.49 % Rotamer: Outliers : 0.54 % Allowed : 4.35 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.21), residues: 1594 helix: 2.91 (0.18), residues: 846 sheet: 0.55 (0.43), residues: 148 loop : -0.67 (0.23), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 976 HIS 0.002 0.001 HIS B 679 PHE 0.013 0.001 PHE B 984 TYR 0.010 0.001 TYR B 511 ARG 0.003 0.000 ARG B 446 Details of bonding type rmsd hydrogen bonds : bond 0.05249 ( 759) hydrogen bonds : angle 4.00357 ( 2169) covalent geometry : bond 0.00359 (13258) covalent geometry : angle 0.42036 (17952) *********************** 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 70 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 1.851 Fit side-chains REVERT: A 430 MET cc_start: 0.8795 (mmm) cc_final: 0.8498 (mmm) REVERT: A 494 GLU cc_start: 0.8899 (OUTLIER) cc_final: 0.7999 (tt0) REVERT: A 699 TYR cc_start: 0.9041 (OUTLIER) cc_final: 0.8056 (t80) REVERT: A 882 ASP cc_start: 0.7896 (m-30) cc_final: 0.6672 (p0) REVERT: B 430 MET cc_start: 0.8802 (mmm) cc_final: 0.8501 (mmm) REVERT: B 494 GLU cc_start: 0.8910 (OUTLIER) cc_final: 0.8007 (tt0) REVERT: B 699 TYR cc_start: 0.9037 (OUTLIER) cc_final: 0.8051 (t80) outliers start: 7 outliers final: 1 residues processed: 69 average time/residue: 0.4883 time to fit residues: 57.0509 Evaluate side-chains 66 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 2.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 699 TYR Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 699 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 16 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 35 optimal weight: 0.0060 chunk 120 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 overall best weight: 1.2004 ------------------------------------------------------------------------------- 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 = 0.3533 r_free = 0.3533 target = 0.110775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.077184 restraints weight = 55840.788| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.43 r_work: 0.2822 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 13258 Z= 0.103 Angle : 0.393 4.464 17952 Z= 0.215 Chirality : 0.037 0.138 1986 Planarity : 0.003 0.030 2220 Dihedral : 10.256 86.851 2156 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.25 % Allowed : 2.32 % Favored : 97.43 % Rotamer: Outliers : 0.54 % Allowed : 4.43 % Favored : 95.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.21), residues: 1594 helix: 3.03 (0.18), residues: 848 sheet: 0.57 (0.43), residues: 148 loop : -0.67 (0.23), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 976 HIS 0.002 0.000 HIS A 303 PHE 0.010 0.001 PHE B 984 TYR 0.009 0.001 TYR B 511 ARG 0.002 0.000 ARG A 446 Details of bonding type rmsd hydrogen bonds : bond 0.04671 ( 759) hydrogen bonds : angle 3.89260 ( 2169) covalent geometry : bond 0.00223 (13258) covalent geometry : angle 0.39253 (17952) *********************** 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 70 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 2.155 Fit side-chains REVERT: A 494 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.7952 (tt0) REVERT: A 699 TYR cc_start: 0.8975 (OUTLIER) cc_final: 0.8075 (t80) REVERT: A 882 ASP cc_start: 0.7907 (m-30) cc_final: 0.6688 (p0) REVERT: B 494 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.7943 (tt0) REVERT: B 699 TYR cc_start: 0.8979 (OUTLIER) cc_final: 0.8082 (t80) outliers start: 7 outliers final: 1 residues processed: 69 average time/residue: 0.4369 time to fit residues: 50.3357 Evaluate side-chains 65 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 2.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 699 TYR Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 699 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 108 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 156 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 138 optimal weight: 9.9990 chunk 15 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 69 optimal weight: 6.9990 chunk 84 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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 = 0.109329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.074565 restraints weight = 56647.954| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 2.53 r_work: 0.2774 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2636 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.3655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 13258 Z= 0.222 Angle : 0.458 4.691 17952 Z= 0.254 Chirality : 0.040 0.142 1986 Planarity : 0.003 0.032 2220 Dihedral : 10.799 87.349 2156 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.39 % Favored : 96.36 % Rotamer: Outliers : 0.54 % Allowed : 4.35 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.21), residues: 1594 helix: 2.78 (0.17), residues: 846 sheet: 0.41 (0.43), residues: 148 loop : -0.70 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 693 HIS 0.003 0.001 HIS A 400 PHE 0.017 0.001 PHE A 984 TYR 0.012 0.001 TYR B 511 ARG 0.004 0.001 ARG B 446 Details of bonding type rmsd hydrogen bonds : bond 0.05815 ( 759) hydrogen bonds : angle 4.10478 ( 2169) covalent geometry : bond 0.00532 (13258) covalent geometry : angle 0.45849 (17952) *********************** 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 71 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 1.913 Fit side-chains REVERT: A 494 GLU cc_start: 0.8913 (OUTLIER) cc_final: 0.8075 (tt0) REVERT: A 699 TYR cc_start: 0.9078 (OUTLIER) cc_final: 0.8094 (t80) REVERT: B 494 GLU cc_start: 0.8906 (OUTLIER) cc_final: 0.8070 (tt0) REVERT: B 699 TYR cc_start: 0.9077 (OUTLIER) cc_final: 0.8094 (t80) outliers start: 7 outliers final: 1 residues processed: 70 average time/residue: 0.4381 time to fit residues: 51.0704 Evaluate side-chains 66 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 2.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 699 TYR Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 699 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 134 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 62 optimal weight: 0.1980 chunk 79 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 142 optimal weight: 0.7980 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.111452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.078566 restraints weight = 55661.888| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 2.39 r_work: 0.2809 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2670 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 13258 Z= 0.098 Angle : 0.396 4.489 17952 Z= 0.217 Chirality : 0.037 0.138 1986 Planarity : 0.003 0.031 2220 Dihedral : 10.451 87.638 2156 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.25 % Allowed : 2.38 % Favored : 97.37 % Rotamer: Outliers : 0.39 % Allowed : 4.58 % Favored : 95.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.21), residues: 1594 helix: 3.02 (0.18), residues: 846 sheet: 0.48 (0.43), residues: 148 loop : -0.63 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 976 HIS 0.002 0.000 HIS A 303 PHE 0.010 0.001 PHE A 984 TYR 0.008 0.001 TYR A 319 ARG 0.002 0.000 ARG A 646 Details of bonding type rmsd hydrogen bonds : bond 0.04732 ( 759) hydrogen bonds : angle 3.91162 ( 2169) covalent geometry : bond 0.00205 (13258) covalent geometry : angle 0.39557 (17952) ********************** 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 66 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 1.928 Fit side-chains REVERT: A 494 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.7997 (tt0) REVERT: A 699 TYR cc_start: 0.8974 (OUTLIER) cc_final: 0.8079 (t80) REVERT: B 494 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.7996 (tt0) REVERT: B 699 TYR cc_start: 0.8969 (OUTLIER) cc_final: 0.8073 (t80) outliers start: 5 outliers final: 1 residues processed: 65 average time/residue: 0.4407 time to fit residues: 47.3028 Evaluate side-chains 66 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 1.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 699 TYR Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 699 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 30 optimal weight: 0.0770 chunk 157 optimal weight: 1.9990 chunk 82 optimal weight: 9.9990 chunk 37 optimal weight: 8.9990 chunk 21 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 133 optimal weight: 2.9990 chunk 18 optimal weight: 0.0000 chunk 99 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 overall best weight: 0.9946 ------------------------------------------------------------------------------- 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 = 0.3540 r_free = 0.3540 target = 0.111263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.077891 restraints weight = 55649.561| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 2.42 r_work: 0.2837 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2700 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 13258 Z= 0.099 Angle : 0.387 4.797 17952 Z= 0.211 Chirality : 0.037 0.138 1986 Planarity : 0.002 0.031 2220 Dihedral : 10.157 85.685 2156 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.26 % Favored : 96.49 % Rotamer: Outliers : 0.39 % Allowed : 4.58 % Favored : 95.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.21), residues: 1594 helix: 3.15 (0.18), residues: 846 sheet: 0.50 (0.43), residues: 148 loop : -0.62 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 976 HIS 0.002 0.000 HIS B 679 PHE 0.009 0.001 PHE B 984 TYR 0.009 0.001 TYR B 842 ARG 0.002 0.000 ARG B 446 Details of bonding type rmsd hydrogen bonds : bond 0.04387 ( 759) hydrogen bonds : angle 3.80575 ( 2169) covalent geometry : bond 0.00214 (13258) covalent geometry : angle 0.38696 (17952) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12903.71 seconds wall clock time: 222 minutes 56.91 seconds (13376.91 seconds total)