Starting phenix.real_space_refine on Thu Jul 2 22:30:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7myo_24082/07_2026/7myo_24082.cif Found real_map, /net/cci-nas-00/data/ceres_data/7myo_24082/07_2026/7myo_24082.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7myo_24082/07_2026/7myo_24082.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7myo_24082/07_2026/7myo_24082.map" model { file = "/net/cci-nas-00/data/ceres_data/7myo_24082/07_2026/7myo_24082.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7myo_24082/07_2026/7myo_24082.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7myo_24082/07_2026/7myo_24082.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7myo_24082/07_2026/7myo_24082.cif" } resolution = 2.92 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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: 5 Type Number sf(0) Gaussians S 77 5.16 5 C 6763 2.51 5 N 1848 2.21 5 O 1943 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10634 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 2412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2412 Classifications: {'peptide': 286} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 281} Chain: "A" Number of atoms: 8192 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 992, 8107 Classifications: {'peptide': 992} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 945} Chain breaks: 5 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 992, 8107 Classifications: {'peptide': 992} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 945} Chain breaks: 5 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 8193 Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'1LT': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 9 residue: pdb=" N AARG A 617 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 617 " occ=0.50 residue: pdb=" N ALYS A 621 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS A 621 " occ=0.50 residue: pdb=" N AARG A 662 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 662 " occ=0.50 residue: pdb=" N AARG A 899 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 899 " occ=0.50 residue: pdb=" N AARG A 951 " occ=0.63 ... (20 atoms not shown) pdb=" NH2BARG A 951 " occ=0.37 residue: pdb=" N AVAL A 952 " occ=0.63 ... (12 atoms not shown) pdb=" CG2BVAL A 952 " occ=0.37 residue: pdb=" N APRO A 953 " occ=0.63 ... (12 atoms not shown) pdb=" CD BPRO A 953 " occ=0.37 residue: pdb=" N APHE A 954 " occ=0.63 ... (20 atoms not shown) pdb=" CZ BPHE A 954 " occ=0.37 residue: pdb=" N AVAL A 955 " occ=0.63 ... (12 atoms not shown) pdb=" CG2BVAL A 955 " occ=0.37 Time building chain proxies: 3.40, per 1000 atoms: 0.32 Number of scatterers: 10634 At special positions: 0 Unit cell: (89.87, 108.68, 135.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 77 16.00 F 3 9.00 O 1943 8.00 N 1848 7.00 C 6763 6.00 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: 0.84 Conformation dependent library (CDL) restraints added in 749.4 milliseconds 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2466 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 10 sheets defined 50.5% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'B' and resid 339 through 348 Processing helix chain 'B' and resid 385 through 389 removed outlier: 4.091A pdb=" N GLY B 388 " --> pdb=" O HIS B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 411 Processing helix chain 'B' and resid 432 through 436 Processing helix chain 'B' and resid 441 through 506 removed outlier: 3.595A pdb=" N VAL B 445 " --> pdb=" O ASN B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 515 removed outlier: 3.799A pdb=" N PHE B 512 " --> pdb=" O TYR B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 588 removed outlier: 3.927A pdb=" N LEU B 531 " --> pdb=" O ASN B 527 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS B 532 " --> pdb=" O TYR B 528 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP B 548 " --> pdb=" O ARG B 544 " (cutoff:3.500A) Proline residue: B 568 - end of helix Processing helix chain 'B' and resid 593 through 599 removed outlier: 3.915A pdb=" N TRP B 597 " --> pdb=" O LYS B 593 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU B 598 " --> pdb=" O LEU B 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 56 removed outlier: 3.605A pdb=" N HIS A 47 " --> pdb=" O ILE A 43 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N GLU A 48 " --> pdb=" O THR A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 122 removed outlier: 3.815A pdb=" N LYS A 111 " --> pdb=" O ASN A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 131 removed outlier: 3.990A pdb=" N PHE A 128 " --> pdb=" O PRO A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 155 removed outlier: 3.541A pdb=" N GLN A 137 " --> pdb=" O ASP A 133 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU A 144 " --> pdb=" O ARG A 140 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ASN A 145 " --> pdb=" O ARG A 141 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL A 146 " --> pdb=" O ASN A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 167 Processing helix chain 'A' and resid 178 through 183 removed outlier: 3.657A pdb=" N ASN A 183 " --> pdb=" O LYS A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 229 removed outlier: 3.785A pdb=" N VAL A 220 " --> pdb=" O VAL A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 248 Processing helix chain 'A' and resid 270 through 280 Processing helix chain 'A' and resid 290 through 297 Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 326 through 330 removed outlier: 3.690A pdb=" N VAL A 329 " --> pdb=" O SER A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 396 No H-bonds generated for 'chain 'A' and resid 394 through 396' Processing helix chain 'A' and resid 488 through 502 removed outlier: 3.863A pdb=" N ILE A 492 " --> pdb=" O ASP A 488 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL A 500 " --> pdb=" O ALA A 496 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER A 501 " --> pdb=" O ASN A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 536 removed outlier: 3.824A pdb=" N LYS A 528 " --> pdb=" O ARG A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 554 Processing helix chain 'A' and resid 564 through 571 Processing helix chain 'A' and resid 577 through 589 removed outlier: 3.620A pdb=" N ALA A 581 " --> pdb=" O ARG A 577 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP A 589 " --> pdb=" O CYS A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 599 Processing helix chain 'A' and resid 600 through 603 removed outlier: 4.119A pdb=" N ASP A 603 " --> pdb=" O GLU A 600 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 600 through 603' Processing helix chain 'A' and resid 608 through 623 Processing helix chain 'A' and resid 624 through 631 Processing helix chain 'A' and resid 631 through 642 removed outlier: 3.902A pdb=" N LYS A 640 " --> pdb=" O VAL A 636 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N TYR A 641 " --> pdb=" O GLN A 637 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU A 642 " --> pdb=" O VAL A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 658 Processing helix chain 'A' and resid 660 through 673 Processing helix chain 'A' and resid 680 through 695 Processing helix chain 'A' and resid 697 through 721 removed outlier: 3.807A pdb=" N HIS A 701 " --> pdb=" O MET A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 740 Processing helix chain 'A' and resid 741 through 746 Processing helix chain 'A' and resid 747 through 749 No H-bonds generated for 'chain 'A' and resid 747 through 749' Processing helix chain 'A' and resid 787 through 793 removed outlier: 4.438A pdb=" N GLU A 791 " --> pdb=" O ILE A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 828 Processing helix chain 'A' and resid 857 through 867 Processing helix chain 'A' and resid 875 through 885 Processing helix chain 'A' and resid 886 through 888 No H-bonds generated for 'chain 'A' and resid 886 through 888' Processing helix chain 'A' and resid 889 through 911 removed outlier: 4.451A pdb=" N VAL A 906 " --> pdb=" O ALA A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 957 through 965 removed outlier: 3.521A pdb=" N LEU A 961 " --> pdb=" O THR A 957 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER A 965 " --> pdb=" O LEU A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 974 through 993 removed outlier: 4.092A pdb=" N GLU A 978 " --> pdb=" O THR A 974 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ARG A 979 " --> pdb=" O ARG A 975 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1004 removed outlier: 3.696A pdb=" N PHE A 998 " --> pdb=" O HIS A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1019 through 1026 Processing helix chain 'A' and resid 1031 through 1045 Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 355 Processing sheet with id=AA2, first strand: chain 'B' and resid 373 through 374 Processing sheet with id=AA3, first strand: chain 'A' and resid 31 through 36 removed outlier: 3.615A pdb=" N VAL A 32 " --> pdb=" O CYS A 24 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N LEU A 99 " --> pdb=" O LEU A 21 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N GLU A 23 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N VAL A 101 " --> pdb=" O GLU A 23 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU A 25 " --> pdb=" O VAL A 101 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N PHE A 98 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N VAL A 73 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N PHE A 70 " --> pdb=" O PHE A 82 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER A 72 " --> pdb=" O GLU A 80 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 207 through 212 removed outlier: 8.429A pdb=" N LEU A 285 " --> pdb=" O ILE A 191 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N VAL A 193 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N LEU A 287 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS A 253 " --> pdb=" O MET A 286 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LEU A 252 " --> pdb=" O PHE A 261 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 382 through 392 removed outlier: 6.393A pdb=" N TRP A 383 " --> pdb=" O CYS A 340 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N CYS A 340 " --> pdb=" O TRP A 383 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LEU A 334 " --> pdb=" O TYR A 389 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N GLU A 474 " --> pdb=" O LEU A 339 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ALA A 341 " --> pdb=" O CYS A 472 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N CYS A 472 " --> pdb=" O ALA A 341 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 365 through 366 removed outlier: 3.516A pdb=" N VAL A 409 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LYS A 353 " --> pdb=" O VAL A 409 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 365 through 366 removed outlier: 6.430A pdb=" N SER A 408 " --> pdb=" O PRO A 421 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 752 through 753 removed outlier: 5.885A pdb=" N HIS A 759 " --> pdb=" O SER A 753 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 770 through 771 Processing sheet with id=AB1, first strand: chain 'A' and resid 854 through 856 499 hydrogen bonds defined for protein. 1437 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.52 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1774 1.32 - 1.44: 2816 1.44 - 1.56: 6146 1.56 - 1.69: 2 1.69 - 1.81: 121 Bond restraints: 10859 Sorted by residual: bond pdb=" C3 1LT A1101 " pdb=" N1 1LT A1101 " ideal model delta sigma weight residual 1.391 1.485 -0.094 2.00e-02 2.50e+03 2.23e+01 bond pdb=" C2 1LT A1101 " pdb=" N1 1LT A1101 " ideal model delta sigma weight residual 1.368 1.458 -0.090 2.00e-02 2.50e+03 2.04e+01 bond pdb=" C3 1LT A1101 " pdb=" N2 1LT A1101 " ideal model delta sigma weight residual 1.348 1.435 -0.087 2.00e-02 2.50e+03 1.87e+01 bond pdb=" N 1LT A1101 " pdb=" C1 1LT A1101 " ideal model delta sigma weight residual 1.368 1.445 -0.077 2.00e-02 2.50e+03 1.47e+01 bond pdb=" C7 1LT A1101 " pdb=" N2 1LT A1101 " ideal model delta sigma weight residual 1.444 1.520 -0.076 2.00e-02 2.50e+03 1.43e+01 ... (remaining 10854 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 14279 2.57 - 5.14: 306 5.14 - 7.71: 57 7.71 - 10.28: 5 10.28 - 12.86: 4 Bond angle restraints: 14651 Sorted by residual: angle pdb=" N ASP A1017 " pdb=" CA ASP A1017 " pdb=" C ASP A1017 " ideal model delta sigma weight residual 114.31 108.20 6.11 1.29e+00 6.01e-01 2.25e+01 angle pdb=" C ASP A 939 " pdb=" N HIS A 940 " pdb=" CA HIS A 940 " ideal model delta sigma weight residual 121.54 129.94 -8.40 1.91e+00 2.74e-01 1.93e+01 angle pdb=" N GLU B 537 " pdb=" CA GLU B 537 " pdb=" CB GLU B 537 " ideal model delta sigma weight residual 110.30 117.00 -6.70 1.54e+00 4.22e-01 1.90e+01 angle pdb=" CB MET A1040 " pdb=" CG MET A1040 " pdb=" SD MET A1040 " ideal model delta sigma weight residual 112.70 125.56 -12.86 3.00e+00 1.11e-01 1.84e+01 angle pdb=" CG1 ILE A 211 " pdb=" CB ILE A 211 " pdb=" CG2 ILE A 211 " ideal model delta sigma weight residual 110.70 99.90 10.80 3.00e+00 1.11e-01 1.30e+01 ... (remaining 14646 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 5879 17.47 - 34.95: 614 34.95 - 52.42: 113 52.42 - 69.89: 29 69.89 - 87.36: 13 Dihedral angle restraints: 6648 sinusoidal: 2845 harmonic: 3803 Sorted by residual: dihedral pdb=" CA LEU A 209 " pdb=" C LEU A 209 " pdb=" N LYS A 210 " pdb=" CA LYS A 210 " ideal model delta harmonic sigma weight residual -180.00 -153.50 -26.50 0 5.00e+00 4.00e-02 2.81e+01 dihedral pdb=" CA PHE B 512 " pdb=" C PHE B 512 " pdb=" N LYS B 513 " pdb=" CA LYS B 513 " ideal model delta harmonic sigma weight residual 180.00 159.45 20.55 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA LEU A 262 " pdb=" C LEU A 262 " pdb=" N GLU A 263 " pdb=" CA GLU A 263 " ideal model delta harmonic sigma weight residual -180.00 -161.54 -18.46 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 6645 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1062 0.044 - 0.088: 374 0.088 - 0.132: 117 0.132 - 0.175: 19 0.175 - 0.219: 9 Chirality restraints: 1581 Sorted by residual: chirality pdb=" CB ILE A 921 " pdb=" CA ILE A 921 " pdb=" CG1 ILE A 921 " pdb=" CG2 ILE A 921 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA ASN A 202 " pdb=" N ASN A 202 " pdb=" C ASN A 202 " pdb=" CB ASN A 202 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.93e-01 chirality pdb=" CG LEU A 267 " pdb=" CB LEU A 267 " pdb=" CD1 LEU A 267 " pdb=" CD2 LEU A 267 " both_signs ideal model delta sigma weight residual False -2.59 -2.79 0.20 2.00e-01 2.50e+01 9.71e-01 ... (remaining 1578 not shown) Planarity restraints: 1883 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 426 " 0.082 5.00e-02 4.00e+02 1.24e-01 2.44e+01 pdb=" N PRO B 427 " -0.214 5.00e-02 4.00e+02 pdb=" CA PRO B 427 " 0.067 5.00e-02 4.00e+02 pdb=" CD PRO B 427 " 0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 177 " -0.076 5.00e-02 4.00e+02 1.15e-01 2.11e+01 pdb=" N PRO A 178 " 0.198 5.00e-02 4.00e+02 pdb=" CA PRO A 178 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO A 178 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 457 " -0.069 5.00e-02 4.00e+02 1.04e-01 1.72e+01 pdb=" N PRO A 458 " 0.179 5.00e-02 4.00e+02 pdb=" CA PRO A 458 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO A 458 " -0.056 5.00e-02 4.00e+02 ... (remaining 1880 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1491 2.76 - 3.29: 10714 3.29 - 3.83: 18393 3.83 - 4.36: 21335 4.36 - 4.90: 35211 Nonbonded interactions: 87144 Sorted by model distance: nonbonded pdb=" O TYR A1038 " pdb=" OE1 GLN A1042 " model vdw 2.225 3.040 nonbonded pdb=" OH TYR A 988 " pdb=" O LEU A1026 " model vdw 2.247 3.040 nonbonded pdb=" OG SER A 499 " pdb=" OE1 GLN A 582 " model vdw 2.253 3.040 nonbonded pdb=" O ASP A 895 " pdb=" OG1 THR A 898 " model vdw 2.257 3.040 nonbonded pdb=" OE2 GLU B 332 " pdb=" OH TYR B 431 " model vdw 2.268 3.040 ... (remaining 87139 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.37 max=1.00 mean=0.99 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: 0.500 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: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.000 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6558 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 10859 Z= 0.224 Angle : 0.894 12.856 14651 Z= 0.455 Chirality : 0.051 0.219 1581 Planarity : 0.008 0.124 1883 Dihedral : 15.077 87.363 4182 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 0.59 % Allowed : 0.85 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.22), residues: 1281 helix: -0.71 (0.19), residues: 593 sheet: -1.80 (0.43), residues: 137 loop : -1.73 (0.26), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 115 TYR 0.031 0.002 TYR A 165 PHE 0.035 0.003 PHE A 937 TRP 0.059 0.003 TRP B 335 HIS 0.017 0.001 HIS A 940 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.22 (10859) covalent geometry : angle 0.89438 / 0.45 (14651) hydrogen bonds : bond 0.15595 / 10.18 ( 495) hydrogen bonds : angle 6.51487 / 4.52 ( 1437) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 305 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 526 ASN cc_start: 0.7934 (p0) cc_final: 0.7636 (p0) REVERT: A 988 TYR cc_start: 0.5782 (t80) cc_final: 0.5575 (t80) outliers start: 1 outliers final: 0 residues processed: 305 average time/residue: 0.4953 time to fit residues: 164.2502 Evaluate side-chains 210 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 407 HIS ** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 GLN ** A 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 HIS A 426 ASN A 661 GLN A 701 HIS ** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 785 ASN ** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4776 r_free = 0.4776 target = 0.222401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.182719 restraints weight = 45544.055| |-----------------------------------------------------------------------------| r_work (start): 0.4389 rms_B_bonded: 6.09 r_work: 0.4162 rms_B_bonded: 5.72 restraints_weight: 2.0000 r_work (final): 0.4162 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4183 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4183 r_free = 0.4183 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4181 r_free = 0.4181 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.4181 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6929 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10859 Z= 0.162 Angle : 0.757 11.871 14651 Z= 0.380 Chirality : 0.045 0.174 1581 Planarity : 0.006 0.087 1883 Dihedral : 5.222 53.544 1423 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.46 % Allowed : 17.78 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.23), residues: 1281 helix: 0.12 (0.20), residues: 605 sheet: -1.79 (0.43), residues: 142 loop : -1.72 (0.26), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 472 TYR 0.021 0.002 TYR A 432 PHE 0.040 0.002 PHE A 667 TRP 0.021 0.002 TRP B 333 HIS 0.011 0.001 HIS A 940 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 (10859) covalent geometry : angle 0.75719 / 0.38 (14651) hydrogen bonds : bond 0.04367 / 2.88 ( 495) hydrogen bonds : angle 4.95371 / 3.42 ( 1437) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 239 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: B 479 MET cc_start: 0.7504 (pp-130) cc_final: 0.7274 (pp-130) REVERT: A 164 MET cc_start: 0.7786 (mpp) cc_final: 0.6903 (mpt) REVERT: A 330 ILE cc_start: 0.6174 (mt) cc_final: 0.5889 (mt) REVERT: A 391 ILE cc_start: 0.7965 (OUTLIER) cc_final: 0.7603 (tp) REVERT: A 427 ILE cc_start: 0.8544 (mp) cc_final: 0.8142 (mt) REVERT: A 563 GLU cc_start: 0.6725 (tp30) cc_final: 0.5996 (tp30) REVERT: A 979 ARG cc_start: 0.7814 (mtp180) cc_final: 0.7449 (tpt-90) REVERT: A 1000 ASN cc_start: 0.7170 (t0) cc_final: 0.6539 (m-40) REVERT: A 1039 PHE cc_start: 0.6221 (OUTLIER) cc_final: 0.5851 (m-10) outliers start: 23 outliers final: 7 residues processed: 250 average time/residue: 0.4189 time to fit residues: 115.1624 Evaluate side-chains 225 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 216 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain A residue 840 SER Chi-restraints excluded: chain A residue 1039 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 56 optimal weight: 0.5980 chunk 71 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 90 optimal weight: 0.5980 chunk 115 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 499 GLN A 202 ASN ** A 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 701 HIS ** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4741 r_free = 0.4741 target = 0.220140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.179891 restraints weight = 47520.767| |-----------------------------------------------------------------------------| r_work (start): 0.4330 rms_B_bonded: 6.25 r_work: 0.4120 rms_B_bonded: 5.70 restraints_weight: 2.0000 r_work (final): 0.4120 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4145 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4145 r_free = 0.4145 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4145 r_free = 0.4145 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.4145 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 10859 Z= 0.145 Angle : 0.722 10.686 14651 Z= 0.360 Chirality : 0.045 0.293 1581 Planarity : 0.005 0.074 1883 Dihedral : 4.965 52.139 1423 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 3.30 % Allowed : 20.07 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.23), residues: 1281 helix: 0.40 (0.21), residues: 603 sheet: -1.82 (0.42), residues: 142 loop : -1.53 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 141 TYR 0.021 0.002 TYR A 985 PHE 0.044 0.002 PHE A 667 TRP 0.023 0.001 TRP B 333 HIS 0.009 0.001 HIS A 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (10859) covalent geometry : angle 0.72192 / 0.36 (14651) hydrogen bonds : bond 0.03917 / 2.59 ( 495) hydrogen bonds : angle 4.69735 / 3.24 ( 1437) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 232 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: B 367 ASP cc_start: 0.6209 (m-30) cc_final: 0.5972 (m-30) REVERT: B 383 ILE cc_start: 0.7517 (pt) cc_final: 0.7272 (mp) REVERT: B 420 LEU cc_start: 0.6534 (OUTLIER) cc_final: 0.6316 (mm) REVERT: B 479 MET cc_start: 0.7541 (pp-130) cc_final: 0.7114 (pp-130) REVERT: B 499 GLN cc_start: 0.6969 (tm130) cc_final: 0.6645 (tm130) REVERT: A 58 LEU cc_start: 0.6760 (OUTLIER) cc_final: 0.6291 (mm) REVERT: A 164 MET cc_start: 0.7663 (mpp) cc_final: 0.6827 (mpp) REVERT: A 330 ILE cc_start: 0.6467 (mt) cc_final: 0.6164 (mt) REVERT: A 427 ILE cc_start: 0.8564 (mp) cc_final: 0.8167 (mt) REVERT: A 563 GLU cc_start: 0.6680 (tp30) cc_final: 0.6083 (tp30) REVERT: A 760 GLN cc_start: 0.8072 (pt0) cc_final: 0.7605 (pt0) REVERT: A 766 LEU cc_start: 0.8214 (pt) cc_final: 0.7831 (mm) REVERT: A 812 LEU cc_start: 0.7656 (tp) cc_final: 0.7453 (tp) REVERT: A 833 MET cc_start: 0.6322 (ptm) cc_final: 0.5845 (ptt) REVERT: A 979 ARG cc_start: 0.7874 (mtp180) cc_final: 0.7472 (tpt-90) REVERT: A 1000 ASN cc_start: 0.7063 (t0) cc_final: 0.6460 (m-40) outliers start: 33 outliers final: 12 residues processed: 246 average time/residue: 0.4507 time to fit residues: 121.7031 Evaluate side-chains 229 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 215 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 322 MET Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 430 LYS Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain A residue 840 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 31 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 chunk 116 optimal weight: 3.9990 chunk 74 optimal weight: 0.0670 chunk 67 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 chunk 69 optimal weight: 0.8980 overall best weight: 1.3922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 202 ASN ** A 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 634 GLN A 701 HIS ** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 749 GLN A 815 GLN ** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4695 r_free = 0.4695 target = 0.214273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.174569 restraints weight = 48721.062| |-----------------------------------------------------------------------------| r_work (start): 0.4286 rms_B_bonded: 6.15 r_work: 0.4054 rms_B_bonded: 5.78 restraints_weight: 2.0000 r_work (final): 0.4054 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4069 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4069 r_free = 0.4069 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4069 r_free = 0.4069 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.4069 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 10859 Z= 0.175 Angle : 0.726 10.378 14651 Z= 0.366 Chirality : 0.046 0.277 1581 Planarity : 0.005 0.069 1883 Dihedral : 4.964 50.229 1423 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.22 % Allowed : 21.51 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.23), residues: 1281 helix: 0.39 (0.21), residues: 612 sheet: -1.90 (0.42), residues: 142 loop : -1.61 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 141 TYR 0.026 0.002 TYR A 988 PHE 0.042 0.002 PHE A 667 TRP 0.028 0.002 TRP B 333 HIS 0.012 0.001 HIS A 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.18 (10859) covalent geometry : angle 0.72572 / 0.37 (14651) hydrogen bonds : bond 0.03843 / 2.55 ( 495) hydrogen bonds : angle 4.63245 / 3.17 ( 1437) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 245 time to evaluate : 0.340 Fit side-chains REVERT: B 367 ASP cc_start: 0.6355 (m-30) cc_final: 0.6124 (m-30) REVERT: B 420 LEU cc_start: 0.6483 (OUTLIER) cc_final: 0.6158 (mm) REVERT: B 422 VAL cc_start: 0.5910 (OUTLIER) cc_final: 0.5606 (t) REVERT: B 479 MET cc_start: 0.7505 (pp-130) cc_final: 0.7179 (pp-130) REVERT: B 499 GLN cc_start: 0.6843 (tm130) cc_final: 0.6609 (tm130) REVERT: B 534 ARG cc_start: 0.7656 (tpt-90) cc_final: 0.7452 (tpt-90) REVERT: B 537 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7710 (pm20) REVERT: A 58 LEU cc_start: 0.6850 (OUTLIER) cc_final: 0.6304 (mm) REVERT: A 318 MET cc_start: 0.5183 (ttt) cc_final: 0.4784 (mtm) REVERT: A 330 ILE cc_start: 0.6370 (mt) cc_final: 0.5982 (mt) REVERT: A 427 ILE cc_start: 0.8842 (mp) cc_final: 0.8641 (mp) REVERT: A 641 TYR cc_start: 0.7246 (m-10) cc_final: 0.6979 (m-10) REVERT: A 833 MET cc_start: 0.6376 (ptm) cc_final: 0.6051 (ptt) REVERT: A 881 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7852 (tt) REVERT: A 909 PHE cc_start: 0.7910 (t80) cc_final: 0.7592 (t80) REVERT: A 979 ARG cc_start: 0.7925 (mtp180) cc_final: 0.7462 (tpt-90) REVERT: A 1039 PHE cc_start: 0.6552 (m-80) cc_final: 0.6102 (m-80) outliers start: 33 outliers final: 15 residues processed: 260 average time/residue: 0.4117 time to fit residues: 117.9099 Evaluate side-chains 246 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 226 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 322 MET Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 537 GLU Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 891 ASP Chi-restraints excluded: chain A residue 957 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 115 optimal weight: 0.6980 chunk 103 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 42 optimal weight: 7.9990 chunk 46 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 107 optimal weight: 0.0980 chunk 121 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 202 ASN ** A 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4725 r_free = 0.4725 target = 0.217056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.177335 restraints weight = 55464.193| |-----------------------------------------------------------------------------| r_work (start): 0.4309 rms_B_bonded: 6.59 r_work: 0.4083 rms_B_bonded: 5.95 restraints_weight: 2.0000 r_work (final): 0.4083 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4095 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4095 r_free = 0.4095 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4095 r_free = 0.4095 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4095 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10859 Z= 0.137 Angle : 0.723 10.552 14651 Z= 0.358 Chirality : 0.045 0.276 1581 Planarity : 0.005 0.066 1883 Dihedral : 4.826 46.574 1423 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.79 % Allowed : 24.30 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.23), residues: 1281 helix: 0.55 (0.21), residues: 609 sheet: -1.78 (0.42), residues: 139 loop : -1.54 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 141 TYR 0.031 0.002 TYR A 985 PHE 0.053 0.002 PHE A 667 TRP 0.021 0.001 TRP B 333 HIS 0.011 0.001 HIS A 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (10859) covalent geometry : angle 0.72253 / 0.36 (14651) hydrogen bonds : bond 0.03588 / 2.39 ( 495) hydrogen bonds : angle 4.49765 / 3.10 ( 1437) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 237 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 422 VAL cc_start: 0.6231 (OUTLIER) cc_final: 0.5892 (t) REVERT: B 534 ARG cc_start: 0.7778 (tpt-90) cc_final: 0.7459 (tpt-90) REVERT: B 537 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7701 (pm20) REVERT: A 58 LEU cc_start: 0.6905 (OUTLIER) cc_final: 0.6327 (mm) REVERT: A 258 ASP cc_start: 0.8263 (m-30) cc_final: 0.8029 (m-30) REVERT: A 318 MET cc_start: 0.5221 (ttt) cc_final: 0.4810 (mtm) REVERT: A 427 ILE cc_start: 0.8678 (mp) cc_final: 0.8426 (mp) REVERT: A 486 PHE cc_start: 0.6917 (t80) cc_final: 0.6520 (t80) REVERT: A 563 GLU cc_start: 0.6659 (tp30) cc_final: 0.5594 (mm-30) REVERT: A 760 GLN cc_start: 0.7947 (pt0) cc_final: 0.7596 (pt0) REVERT: A 833 MET cc_start: 0.6442 (ptm) cc_final: 0.5981 (ptt) REVERT: A 979 ARG cc_start: 0.7938 (mtp180) cc_final: 0.7480 (tpt-90) REVERT: A 1000 ASN cc_start: 0.7109 (t0) cc_final: 0.6776 (m-40) REVERT: A 1039 PHE cc_start: 0.6620 (m-80) cc_final: 0.6197 (m-80) outliers start: 28 outliers final: 14 residues processed: 254 average time/residue: 0.4092 time to fit residues: 114.5690 Evaluate side-chains 238 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 221 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 322 MET Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 430 LYS Chi-restraints excluded: chain B residue 537 GLU Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 840 SER Chi-restraints excluded: chain A residue 859 GLN Chi-restraints excluded: chain A residue 957 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 44 optimal weight: 0.0470 chunk 13 optimal weight: 5.9990 chunk 68 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 18 optimal weight: 9.9990 chunk 58 optimal weight: 0.6980 chunk 27 optimal weight: 4.9990 chunk 100 optimal weight: 8.9990 chunk 96 optimal weight: 3.9990 chunk 108 optimal weight: 0.4980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4719 r_free = 0.4719 target = 0.216990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.178957 restraints weight = 42390.489| |-----------------------------------------------------------------------------| r_work (start): 0.4339 rms_B_bonded: 5.14 r_work: 0.4131 rms_B_bonded: 5.11 restraints_weight: 2.0000 r_work (final): 0.4131 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4146 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4146 r_free = 0.4146 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4146 r_free = 0.4146 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4146 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6922 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 10859 Z= 0.143 Angle : 0.731 10.281 14651 Z= 0.365 Chirality : 0.045 0.253 1581 Planarity : 0.005 0.064 1883 Dihedral : 4.776 44.382 1423 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.96 % Allowed : 25.40 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.23), residues: 1281 helix: 0.59 (0.21), residues: 603 sheet: -1.92 (0.41), residues: 142 loop : -1.50 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 141 TYR 0.043 0.002 TYR A 432 PHE 0.051 0.002 PHE A 667 TRP 0.042 0.002 TRP B 333 HIS 0.012 0.001 HIS A 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 (10859) covalent geometry : angle 0.73091 / 0.36 (14651) hydrogen bonds : bond 0.03535 / 2.36 ( 495) hydrogen bonds : angle 4.52506 / 3.10 ( 1437) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 234 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 422 VAL cc_start: 0.6179 (OUTLIER) cc_final: 0.5805 (t) REVERT: B 479 MET cc_start: 0.7435 (pp-130) cc_final: 0.7077 (pp-130) REVERT: B 534 ARG cc_start: 0.7760 (tpt-90) cc_final: 0.7417 (tpt-90) REVERT: B 537 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7705 (pm20) REVERT: A 58 LEU cc_start: 0.7037 (OUTLIER) cc_final: 0.6377 (mm) REVERT: A 258 ASP cc_start: 0.8251 (m-30) cc_final: 0.7983 (m-30) REVERT: A 296 GLN cc_start: 0.7642 (tp40) cc_final: 0.7363 (tp40) REVERT: A 318 MET cc_start: 0.5070 (ttt) cc_final: 0.4688 (mtm) REVERT: A 427 ILE cc_start: 0.8634 (mp) cc_final: 0.8212 (mt) REVERT: A 486 PHE cc_start: 0.6854 (t80) cc_final: 0.6594 (t80) REVERT: A 760 GLN cc_start: 0.7869 (pt0) cc_final: 0.7423 (pt0) REVERT: A 833 MET cc_start: 0.6477 (ptm) cc_final: 0.6088 (ptt) REVERT: A 875 HIS cc_start: 0.7624 (m-70) cc_final: 0.6572 (p-80) REVERT: A 979 ARG cc_start: 0.7806 (mtp180) cc_final: 0.7401 (tpt-90) REVERT: A 1000 ASN cc_start: 0.6961 (t0) cc_final: 0.6593 (m-40) REVERT: A 1039 PHE cc_start: 0.6550 (OUTLIER) cc_final: 0.6299 (m-80) outliers start: 29 outliers final: 15 residues processed: 251 average time/residue: 0.4231 time to fit residues: 116.7213 Evaluate side-chains 240 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 221 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 322 MET Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 430 LYS Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 537 GLU Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 859 GLN Chi-restraints excluded: chain A residue 891 ASP Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 1039 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 26 optimal weight: 9.9990 chunk 45 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 59 optimal weight: 0.0040 chunk 41 optimal weight: 2.9990 chunk 118 optimal weight: 0.0050 chunk 95 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 overall best weight: 1.2010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 586 GLN ** A 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 202 ASN ** A 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 993 GLN A1042 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4703 r_free = 0.4703 target = 0.214637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.176643 restraints weight = 40229.897| |-----------------------------------------------------------------------------| r_work (start): 0.4398 rms_B_bonded: 4.89 r_work (final): 0.4398 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4396 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4396 r_free = 0.4396 target_work(ls_wunit_k1) = 0.179 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4395 r_free = 0.4395 target_work(ls_wunit_k1) = 0.179 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.4395 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6836 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 10859 Z= 0.166 Angle : 0.756 9.972 14651 Z= 0.376 Chirality : 0.047 0.314 1581 Planarity : 0.005 0.063 1883 Dihedral : 4.821 41.564 1423 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 17.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 3.47 % Allowed : 25.40 % Favored : 71.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.23), residues: 1281 helix: 0.58 (0.21), residues: 599 sheet: -2.09 (0.40), residues: 145 loop : -1.36 (0.27), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1023 TYR 0.034 0.002 TYR A 432 PHE 0.047 0.002 PHE A 667 TRP 0.039 0.002 TRP B 333 HIS 0.009 0.001 HIS A 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 (10859) covalent geometry : angle 0.75616 / 0.38 (14651) hydrogen bonds : bond 0.03651 / 2.44 ( 495) hydrogen bonds : angle 4.56391 / 3.13 ( 1437) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 223 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 422 VAL cc_start: 0.6272 (OUTLIER) cc_final: 0.5885 (t) REVERT: B 424 LEU cc_start: 0.6694 (tp) cc_final: 0.6489 (tp) REVERT: B 479 MET cc_start: 0.6980 (pp-130) cc_final: 0.6601 (pp-130) REVERT: B 534 ARG cc_start: 0.7934 (tpt-90) cc_final: 0.7685 (tpt-90) REVERT: B 537 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7586 (pm20) REVERT: A 58 LEU cc_start: 0.6900 (OUTLIER) cc_final: 0.6343 (mm) REVERT: A 427 ILE cc_start: 0.8581 (mp) cc_final: 0.8176 (mt) REVERT: A 441 MET cc_start: 0.6686 (ppp) cc_final: 0.6342 (ppp) REVERT: A 760 GLN cc_start: 0.7462 (pt0) cc_final: 0.7151 (pt0) REVERT: A 833 MET cc_start: 0.5978 (ptm) cc_final: 0.5547 (ptt) REVERT: A 875 HIS cc_start: 0.7491 (m-70) cc_final: 0.6619 (p-80) REVERT: A 909 PHE cc_start: 0.7679 (t80) cc_final: 0.7462 (t80) REVERT: A 979 ARG cc_start: 0.7603 (mtp180) cc_final: 0.7214 (tpt-90) REVERT: A 1000 ASN cc_start: 0.6606 (t0) cc_final: 0.6334 (m-40) REVERT: A 1042 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.8108 (mp10) outliers start: 35 outliers final: 21 residues processed: 243 average time/residue: 0.4098 time to fit residues: 109.8046 Evaluate side-chains 237 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 212 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 322 MET Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 430 LYS Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 537 GLU Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 859 GLN Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 993 GLN Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1042 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 16 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 93 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 98 optimal weight: 0.0770 chunk 5 optimal weight: 0.9990 chunk 119 optimal weight: 7.9990 chunk 90 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 chunk 126 optimal weight: 4.9990 chunk 115 optimal weight: 0.9980 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 586 GLN ** A 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 827 GLN ** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 993 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4712 r_free = 0.4712 target = 0.215944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.176497 restraints weight = 51098.619| |-----------------------------------------------------------------------------| r_work (start): 0.4306 rms_B_bonded: 6.21 r_work: 0.4087 rms_B_bonded: 5.62 restraints_weight: 2.0000 r_work (final): 0.4087 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4099 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4099 r_free = 0.4099 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4099 r_free = 0.4099 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.4099 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10859 Z= 0.150 Angle : 0.774 11.173 14651 Z= 0.382 Chirality : 0.047 0.315 1581 Planarity : 0.005 0.062 1883 Dihedral : 4.795 40.628 1423 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 2.88 % Allowed : 26.76 % Favored : 70.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.24), residues: 1281 helix: 0.61 (0.21), residues: 601 sheet: -1.97 (0.40), residues: 142 loop : -1.42 (0.27), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1023 TYR 0.034 0.002 TYR A 432 PHE 0.047 0.002 PHE A 667 TRP 0.045 0.002 TRP B 333 HIS 0.008 0.001 HIS A 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (10859) covalent geometry : angle 0.77363 / 0.38 (14651) hydrogen bonds : bond 0.03604 / 2.41 ( 495) hydrogen bonds : angle 4.54767 / 3.13 ( 1437) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 223 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 403 GLU cc_start: 0.7484 (pp20) cc_final: 0.7132 (pm20) REVERT: B 422 VAL cc_start: 0.6219 (OUTLIER) cc_final: 0.5865 (t) REVERT: B 479 MET cc_start: 0.7454 (pp-130) cc_final: 0.7106 (pp-130) REVERT: B 537 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7705 (pm20) REVERT: B 563 MET cc_start: 0.6332 (ppp) cc_final: 0.4451 (mtm) REVERT: A 58 LEU cc_start: 0.7170 (OUTLIER) cc_final: 0.6457 (mm) REVERT: A 296 GLN cc_start: 0.7435 (tp40) cc_final: 0.6075 (mt0) REVERT: A 427 ILE cc_start: 0.8727 (mp) cc_final: 0.8296 (mt) REVERT: A 599 MET cc_start: 0.7060 (mtm) cc_final: 0.6809 (mtt) REVERT: A 620 GLU cc_start: 0.7218 (pp20) cc_final: 0.6829 (tt0) REVERT: A 833 MET cc_start: 0.6576 (ptm) cc_final: 0.6199 (ptt) REVERT: A 875 HIS cc_start: 0.7701 (m-70) cc_final: 0.6585 (p-80) REVERT: A 909 PHE cc_start: 0.8042 (t80) cc_final: 0.7776 (t80) REVERT: A 1000 ASN cc_start: 0.7066 (t0) cc_final: 0.6792 (m-40) REVERT: A 1039 PHE cc_start: 0.6654 (m-80) cc_final: 0.6351 (m-80) outliers start: 28 outliers final: 19 residues processed: 240 average time/residue: 0.4094 time to fit residues: 108.2634 Evaluate side-chains 238 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 216 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 322 MET Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 430 LYS Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 537 GLU Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 859 GLN Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 993 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 44 optimal weight: 0.0040 chunk 26 optimal weight: 10.0000 chunk 38 optimal weight: 0.2980 chunk 87 optimal weight: 0.6980 chunk 51 optimal weight: 0.4980 chunk 40 optimal weight: 0.8980 chunk 121 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 66 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 586 GLN A 202 ASN ** A 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 827 GLN ** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 981 GLN A 993 GLN A1042 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4731 r_free = 0.4731 target = 0.217605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.178973 restraints weight = 46926.987| |-----------------------------------------------------------------------------| r_work (start): 0.4341 rms_B_bonded: 5.55 r_work: 0.4129 rms_B_bonded: 5.28 restraints_weight: 2.0000 r_work (final): 0.4129 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4141 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4141 r_free = 0.4141 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4141 r_free = 0.4141 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4141 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 10859 Z= 0.142 Angle : 0.774 10.333 14651 Z= 0.382 Chirality : 0.046 0.295 1581 Planarity : 0.005 0.062 1883 Dihedral : 4.762 39.100 1423 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.62 % Allowed : 27.27 % Favored : 70.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.24), residues: 1281 helix: 0.68 (0.21), residues: 595 sheet: -1.92 (0.40), residues: 142 loop : -1.30 (0.28), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1023 TYR 0.034 0.002 TYR A 985 PHE 0.048 0.002 PHE A 667 TRP 0.041 0.002 TRP B 333 HIS 0.008 0.001 HIS A 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (10859) covalent geometry : angle 0.77400 / 0.38 (14651) hydrogen bonds : bond 0.03574 / 2.42 ( 495) hydrogen bonds : angle 4.53598 / 3.12 ( 1437) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 226 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 326 MET cc_start: 0.5847 (OUTLIER) cc_final: 0.5600 (ppp) REVERT: B 403 GLU cc_start: 0.7496 (pp20) cc_final: 0.7183 (pm20) REVERT: B 420 LEU cc_start: 0.6491 (mm) cc_final: 0.6187 (mm) REVERT: B 422 VAL cc_start: 0.6209 (OUTLIER) cc_final: 0.5872 (t) REVERT: B 479 MET cc_start: 0.7418 (pp-130) cc_final: 0.7024 (pp-130) REVERT: B 480 LYS cc_start: 0.8699 (mttt) cc_final: 0.8398 (mttt) REVERT: B 512 PHE cc_start: 0.5993 (t80) cc_final: 0.5790 (t80) REVERT: A 58 LEU cc_start: 0.7144 (OUTLIER) cc_final: 0.6453 (mm) REVERT: A 164 MET cc_start: 0.7820 (mpp) cc_final: 0.7435 (mpt) REVERT: A 296 GLN cc_start: 0.7493 (tp40) cc_final: 0.6140 (mt0) REVERT: A 427 ILE cc_start: 0.8632 (mp) cc_final: 0.8239 (mt) REVERT: A 599 MET cc_start: 0.6980 (mtm) cc_final: 0.6741 (mtt) REVERT: A 833 MET cc_start: 0.6517 (ptm) cc_final: 0.6150 (ptt) REVERT: A 875 HIS cc_start: 0.7557 (m-70) cc_final: 0.6505 (p-80) REVERT: A 909 PHE cc_start: 0.7964 (t80) cc_final: 0.7754 (t80) REVERT: A 979 ARG cc_start: 0.7745 (mtp85) cc_final: 0.7194 (tpt-90) REVERT: A 993 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7952 (mp10) REVERT: A 1000 ASN cc_start: 0.6928 (t0) cc_final: 0.6633 (m-40) REVERT: A 1039 PHE cc_start: 0.6607 (m-80) cc_final: 0.6337 (m-80) outliers start: 25 outliers final: 16 residues processed: 243 average time/residue: 0.4264 time to fit residues: 113.8545 Evaluate side-chains 232 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 212 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 322 MET Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 430 LYS Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 537 GLU Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 859 GLN Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 993 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 120 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 66 optimal weight: 0.0970 chunk 36 optimal weight: 0.0040 chunk 75 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 48 optimal weight: 0.0170 chunk 124 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 overall best weight: 0.3828 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 586 GLN A 202 ASN ** A 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 827 GLN ** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 993 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1042 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4728 r_free = 0.4728 target = 0.217817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.179730 restraints weight = 43220.559| |-----------------------------------------------------------------------------| r_work (start): 0.4360 rms_B_bonded: 5.17 r_work: 0.4152 rms_B_bonded: 5.11 restraints_weight: 2.0000 r_work (final): 0.4152 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4153 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4153 r_free = 0.4153 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4153 r_free = 0.4153 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4153 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6929 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.180 10859 Z= 0.262 Angle : 1.056 59.058 14651 Z= 0.589 Chirality : 0.054 1.093 1581 Planarity : 0.006 0.178 1883 Dihedral : 4.752 39.094 1423 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 18.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 2.37 % Allowed : 28.03 % Favored : 69.60 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.24), residues: 1281 helix: 0.68 (0.21), residues: 595 sheet: -1.92 (0.40), residues: 142 loop : -1.33 (0.28), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 401 TYR 0.029 0.002 TYR A 432 PHE 0.046 0.002 PHE A 667 TRP 0.038 0.002 TRP B 333 HIS 0.007 0.001 HIS A 940 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.26 (10859) covalent geometry : angle 1.05571 / 0.59 (14651) hydrogen bonds : bond 0.03564 / 2.41 ( 495) hydrogen bonds : angle 4.54209 / 3.13 ( 1437) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 211 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 403 GLU cc_start: 0.7485 (pp20) cc_final: 0.7176 (pm20) REVERT: B 420 LEU cc_start: 0.6395 (mm) cc_final: 0.6092 (mm) REVERT: B 422 VAL cc_start: 0.6181 (OUTLIER) cc_final: 0.5857 (t) REVERT: B 479 MET cc_start: 0.7436 (pp-130) cc_final: 0.7091 (pp-130) REVERT: A 58 LEU cc_start: 0.7140 (OUTLIER) cc_final: 0.6444 (mm) REVERT: A 164 MET cc_start: 0.7801 (mpp) cc_final: 0.7417 (mpt) REVERT: A 296 GLN cc_start: 0.7468 (tp40) cc_final: 0.6148 (mt0) REVERT: A 427 ILE cc_start: 0.8613 (mp) cc_final: 0.8218 (mt) REVERT: A 599 MET cc_start: 0.7012 (mtm) cc_final: 0.6779 (mtt) REVERT: A 833 MET cc_start: 0.6389 (ptm) cc_final: 0.6043 (ptt) REVERT: A 875 HIS cc_start: 0.7537 (m-70) cc_final: 0.6513 (p-80) REVERT: A 909 PHE cc_start: 0.8027 (t80) cc_final: 0.7801 (t80) REVERT: A 979 ARG cc_start: 0.7674 (mtp85) cc_final: 0.7181 (tpt-90) REVERT: A 1000 ASN cc_start: 0.6895 (t0) cc_final: 0.6636 (m-40) REVERT: A 1039 PHE cc_start: 0.6583 (m-80) cc_final: 0.6235 (m-80) outliers start: 22 outliers final: 15 residues processed: 226 average time/residue: 0.4180 time to fit residues: 104.7087 Evaluate side-chains 226 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 209 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 322 MET Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 430 LYS Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 537 GLU Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 859 GLN Chi-restraints excluded: chain A residue 957 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 11 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 104 optimal weight: 0.8980 chunk 92 optimal weight: 0.8980 chunk 102 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 827 GLN ** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 993 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4730 r_free = 0.4730 target = 0.217732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.178888 restraints weight = 47031.266| |-----------------------------------------------------------------------------| r_work (start): 0.4421 rms_B_bonded: 5.46 r_work: 0.4203 rms_B_bonded: 5.23 restraints_weight: 2.0000 r_work (final): 0.4203 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4145 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4145 r_free = 0.4145 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4145 r_free = 0.4145 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4145 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.163 10859 Z= 0.211 Angle : 1.003 59.199 14651 Z= 0.539 Chirality : 0.047 0.460 1581 Planarity : 0.005 0.089 1883 Dihedral : 4.788 39.072 1423 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 18.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.54 % Favored : 94.38 % Rotamer: Outliers : 2.37 % Allowed : 27.86 % Favored : 69.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.24), residues: 1281 helix: 0.67 (0.21), residues: 596 sheet: -1.88 (0.40), residues: 144 loop : -1.34 (0.28), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 401 TYR 0.027 0.002 TYR A 432 PHE 0.045 0.002 PHE A 667 TRP 0.034 0.001 TRP B 333 HIS 0.008 0.001 HIS A 940 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.21 (10859) covalent geometry : angle 1.00302 / 0.54 (14651) hydrogen bonds : bond 0.03569 / 2.41 ( 495) hydrogen bonds : angle 4.53936 / 3.12 ( 1437) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3923.43 seconds wall clock time: 67 minutes 54.18 seconds (4074.18 seconds total)