Starting phenix.real_space_refine on Wed Feb 4 12:24:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lwr_63457/02_2026/9lwr_63457.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lwr_63457/02_2026/9lwr_63457.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lwr_63457/02_2026/9lwr_63457.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lwr_63457/02_2026/9lwr_63457.map" model { file = "/net/cci-nas-00/data/ceres_data/9lwr_63457/02_2026/9lwr_63457.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lwr_63457/02_2026/9lwr_63457.cif" } resolution = 3.3 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= -0.001 sd= 0.039 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: 4 Type Number sf(0) Gaussians S 73 5.16 5 C 6607 2.51 5 N 1798 2.21 5 O 1920 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 65 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10398 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7991 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 978, 7987 Classifications: {'peptide': 978} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 46, 'TRANS': 930} Chain breaks: 6 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Conformer: "B" Number of residues, atoms: 978, 7987 Classifications: {'peptide': 978} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 46, 'TRANS': 930} Chain breaks: 6 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 bond proxies already assigned to first conformer: 8156 Chain: "B" Number of atoms: 2399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2399 Classifications: {'peptide': 283} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 278} Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AGLY A 935 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY A 935 " occ=0.50 Time building chain proxies: 3.15, per 1000 atoms: 0.30 Number of scatterers: 10398 At special positions: 0 Unit cell: (89.964, 123.165, 114.597, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 73 16.00 O 1920 8.00 N 1798 7.00 C 6607 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: 0.60 Conformation dependent library (CDL) restraints added in 755.9 milliseconds 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2414 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 10 sheets defined 52.0% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 41 through 53 Processing helix chain 'A' and resid 64 through 68 Processing helix chain 'A' and resid 89 through 93 Processing helix chain 'A' and resid 107 through 122 Processing helix chain 'A' and resid 125 through 131 removed outlier: 3.902A pdb=" N ASP A 129 " --> pdb=" O VAL A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 155 removed outlier: 4.191A pdb=" N LEU A 144 " --> pdb=" O ARG A 140 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ASN A 145 " --> pdb=" O ARG A 141 " (cutoff:3.500A) removed outlier: 4.209A 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 Processing helix chain 'A' and resid 216 through 229 Processing helix chain 'A' and resid 270 through 280 Processing helix chain 'A' and resid 290 through 297 Processing helix chain 'A' and resid 305 through 310 removed outlier: 4.260A pdb=" N ARG A 309 " --> pdb=" O PRO A 305 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG A 310 " --> pdb=" O SER A 306 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 305 through 310' Processing helix chain 'A' and resid 328 through 330 No H-bonds generated for 'chain 'A' and resid 328 through 330' Processing helix chain 'A' and resid 488 through 496 Processing helix chain 'A' and resid 527 through 537 Processing helix chain 'A' and resid 544 through 554 Processing helix chain 'A' and resid 555 through 563 removed outlier: 4.008A pdb=" N VAL A 559 " --> pdb=" O HIS A 556 " (cutoff:3.500A) Proline residue: A 562 - end of helix Processing helix chain 'A' and resid 564 through 572 Processing helix chain 'A' and resid 576 through 589 Processing helix chain 'A' and resid 594 through 599 Processing helix 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 638 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 694 Processing helix chain 'A' and resid 697 through 722 removed outlier: 4.242A pdb=" N HIS A 701 " --> pdb=" O MET A 697 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU A 722 " --> pdb=" O ILE A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 741 Processing helix chain 'A' and resid 741 through 749 Processing helix chain 'A' and resid 807 through 828 Processing helix chain 'A' and resid 857 through 863 Processing helix chain 'A' and resid 875 through 885 Processing helix chain 'A' and resid 888 through 912 removed outlier: 3.989A pdb=" N ALA A 892 " --> pdb=" O GLU A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 919 No H-bonds generated for 'chain 'A' and resid 917 through 919' Processing helix chain 'A' and resid 938 through 942 removed outlier: 4.021A pdb=" N LYS A 941 " --> pdb=" O LEU A 938 " (cutoff:3.500A) Processing helix chain 'A' and resid 957 through 965 Processing helix chain 'A' and resid 970 through 973 Processing helix chain 'A' and resid 974 through 994 removed outlier: 4.000A pdb=" N GLU A 978 " --> pdb=" O THR A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1005 removed outlier: 3.810A pdb=" N PHE A 998 " --> pdb=" O HIS A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1006 through 1009 removed outlier: 4.173A pdb=" N GLY A1009 " --> pdb=" O LEU A1006 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1006 through 1009' Processing helix chain 'A' and resid 1019 through 1027 removed outlier: 3.925A pdb=" N ARG A1023 " --> pdb=" O ILE A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1031 through 1048 Processing helix chain 'B' and resid 339 through 347 Processing helix chain 'B' and resid 400 through 411 Processing helix chain 'B' and resid 430 through 437 removed outlier: 3.684A pdb=" N VAL B 437 " --> pdb=" O GLN B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 516 removed outlier: 4.311A pdb=" N GLU B 507 " --> pdb=" O ARG B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 586 Proline residue: B 568 - end of helix Processing helix chain 'B' and resid 590 through 599 removed outlier: 4.200A pdb=" N GLY B 599 " --> pdb=" O ASN B 595 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 36 removed outlier: 3.694A pdb=" N VAL A 32 " --> pdb=" O CYS A 24 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE A 20 " --> pdb=" O CYS A 36 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N PHE A 98 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N VAL A 73 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE A 70 " --> pdb=" O PHE A 82 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 205 through 212 removed outlier: 3.656A pdb=" N GLN A 205 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N LEU A 285 " --> pdb=" O ILE A 191 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL A 193 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N LEU A 287 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N TRP A 195 " --> pdb=" O LEU A 287 " (cutoff:3.500A) removed outlier: 9.271A pdb=" N ALA A 289 " --> pdb=" O TRP A 195 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LEU A 252 " --> pdb=" O PHE A 261 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 325 through 326 removed outlier: 6.217A pdb=" N LYS A 325 " --> pdb=" O LYS A 485 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 382 through 392 removed outlier: 6.766A pdb=" N TRP A 383 " --> pdb=" O CYS A 340 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N CYS A 340 " --> pdb=" O TRP A 383 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU A 334 " --> pdb=" O TYR A 389 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N GLU A 474 " --> pdb=" O LEU A 339 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ALA A 341 " --> pdb=" O CYS A 472 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N CYS A 472 " --> pdb=" O ALA A 341 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU A 443 " --> pdb=" O LEU A 473 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET A 441 " --> pdb=" O LEU A 475 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 365 through 372 removed outlier: 3.946A pdb=" N GLU A 365 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ILE A 360 " --> pdb=" O LEU A 367 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N ASP A 369 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N THR A 358 " --> pdb=" O ASP A 369 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N VAL A 371 " --> pdb=" O VAL A 356 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N VAL A 356 " --> pdb=" O VAL A 371 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LYS A 353 " --> pdb=" O VAL A 409 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LEU A 402 " --> pdb=" O ASN A 426 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ASN A 426 " --> pdb=" O LEU A 402 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LEU A 404 " --> pdb=" O TRP A 424 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N TRP A 424 " --> pdb=" O LEU A 404 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE A 406 " --> pdb=" O LEU A 422 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 751 through 752 Processing sheet with id=AA7, first strand: chain 'A' and resid 770 through 771 Processing sheet with id=AA8, first strand: chain 'A' and resid 855 through 856 Processing sheet with id=AA9, first strand: chain 'B' and resid 334 through 336 removed outlier: 3.533A pdb=" N LEU B 356 " --> pdb=" O THR B 371 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG B 358 " --> pdb=" O THR B 369 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR B 369 " --> pdb=" O ARG B 358 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN B 377 " --> pdb=" O LYS B 374 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 384 through 386 527 hydrogen bonds defined for protein. 1524 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: 1.34 Time building geometry restraints manager: 0.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3402 1.34 - 1.46: 1383 1.46 - 1.57: 5706 1.57 - 1.69: 0 1.69 - 1.81: 114 Bond restraints: 10605 Sorted by residual: bond pdb=" CA HIS A 936 " pdb=" C HIS A 936 " ideal model delta sigma weight residual 1.522 1.483 0.039 1.17e-02 7.31e+03 1.12e+01 bond pdb=" CA PHE A 937 " pdb=" C PHE A 937 " ideal model delta sigma weight residual 1.523 1.489 0.035 1.56e-02 4.11e+03 4.91e+00 bond pdb=" CA ASP A 933 " pdb=" C ASP A 933 " ideal model delta sigma weight residual 1.525 1.503 0.022 1.25e-02 6.40e+03 3.14e+00 bond pdb=" CA THR A 33 " pdb=" CB THR A 33 " ideal model delta sigma weight residual 1.526 1.550 -0.024 1.53e-02 4.27e+03 2.41e+00 bond pdb=" CB GLU A 821 " pdb=" CG GLU A 821 " ideal model delta sigma weight residual 1.520 1.477 0.043 3.00e-02 1.11e+03 2.09e+00 ... (remaining 10600 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 13827 1.51 - 3.02: 382 3.02 - 4.53: 66 4.53 - 6.03: 14 6.03 - 7.54: 9 Bond angle restraints: 14298 Sorted by residual: angle pdb=" N ASP A 933 " pdb=" CA ASP A 933 " pdb=" C ASP A 933 " ideal model delta sigma weight residual 108.41 114.81 -6.40 1.61e+00 3.86e-01 1.58e+01 angle pdb=" N ILE A 932 " pdb=" CA ILE A 932 " pdb=" C ILE A 932 " ideal model delta sigma weight residual 109.34 116.18 -6.84 2.08e+00 2.31e-01 1.08e+01 angle pdb=" N LYS A 863 " pdb=" CA LYS A 863 " pdb=" C LYS A 863 " ideal model delta sigma weight residual 110.50 115.07 -4.57 1.41e+00 5.03e-01 1.05e+01 angle pdb=" N SER A 874 " pdb=" CA SER A 874 " pdb=" C SER A 874 " ideal model delta sigma weight residual 113.19 109.46 3.73 1.19e+00 7.06e-01 9.80e+00 angle pdb=" C GLN A1014 " pdb=" N SER A1015 " pdb=" CA SER A1015 " ideal model delta sigma weight residual 121.54 115.57 5.97 1.91e+00 2.74e-01 9.78e+00 ... (remaining 14293 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.02: 5721 18.02 - 36.04: 637 36.04 - 54.06: 102 54.06 - 72.07: 26 72.07 - 90.09: 12 Dihedral angle restraints: 6498 sinusoidal: 2778 harmonic: 3720 Sorted by residual: dihedral pdb=" C ILE A 932 " pdb=" N ILE A 932 " pdb=" CA ILE A 932 " pdb=" CB ILE A 932 " ideal model delta harmonic sigma weight residual -122.00 -132.21 10.21 0 2.50e+00 1.60e-01 1.67e+01 dihedral pdb=" CA GLU A1012 " pdb=" C GLU A1012 " pdb=" N LEU A1013 " pdb=" CA LEU A1013 " ideal model delta harmonic sigma weight residual -180.00 -160.44 -19.56 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA LYS A 621 " pdb=" C LYS A 621 " pdb=" N TYR A 622 " pdb=" CA TYR A 622 " ideal model delta harmonic sigma weight residual -180.00 -160.79 -19.21 0 5.00e+00 4.00e-02 1.48e+01 ... (remaining 6495 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1309 0.061 - 0.121: 214 0.121 - 0.182: 13 0.182 - 0.243: 4 0.243 - 0.303: 4 Chirality restraints: 1544 Sorted by residual: chirality pdb=" CA HIS A1048 " pdb=" N HIS A1048 " pdb=" C HIS A1048 " pdb=" CB HIS A1048 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" CA ILE A 932 " pdb=" N ILE A 932 " pdb=" C ILE A 932 " pdb=" CB ILE A 932 " both_signs ideal model delta sigma weight residual False 2.43 2.13 0.30 2.00e-01 2.50e+01 2.29e+00 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 2.36 0.28 2.00e-01 2.50e+01 1.99e+00 ... (remaining 1541 not shown) Planarity restraints: 1843 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 934 " -0.020 2.00e-02 2.50e+03 3.95e-02 1.56e+01 pdb=" C PHE A 934 " 0.068 2.00e-02 2.50e+03 pdb=" O PHE A 934 " -0.026 2.00e-02 2.50e+03 pdb=" N AGLY A 935 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 934 " -0.020 2.00e-02 2.50e+03 3.94e-02 1.56e+01 pdb=" C PHE A 934 " 0.068 2.00e-02 2.50e+03 pdb=" O PHE A 934 " -0.025 2.00e-02 2.50e+03 pdb=" N BGLY A 935 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 904 " -0.028 2.00e-02 2.50e+03 1.80e-02 6.51e+00 pdb=" CG TYR A 904 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR A 904 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR A 904 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR A 904 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 904 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 904 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 904 " -0.007 2.00e-02 2.50e+03 ... (remaining 1840 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 85 2.58 - 3.16: 8587 3.16 - 3.74: 16487 3.74 - 4.32: 22218 4.32 - 4.90: 37538 Nonbonded interactions: 84915 Sorted by model distance: nonbonded pdb=" OH TYR A 904 " pdb=" O LEU A 929 " model vdw 2.000 3.040 nonbonded pdb=" OD2 ASP A 138 " pdb=" OH TYR A 432 " model vdw 2.234 3.040 nonbonded pdb=" NZ LYS A 337 " pdb=" OD1 ASN A 384 " model vdw 2.247 3.120 nonbonded pdb=" OH TYR A 641 " pdb=" N GLY A1007 " model vdw 2.255 3.120 nonbonded pdb=" NE2 HIS A 495 " pdb=" OD1 ASP A 578 " model vdw 2.266 3.120 ... (remaining 84910 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.990 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: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.630 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6540 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 : 0.004 0.044 10605 Z= 0.178 Angle : 0.640 7.543 14298 Z= 0.359 Chirality : 0.046 0.303 1544 Planarity : 0.005 0.052 1843 Dihedral : 15.321 90.093 4084 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.25 % Favored : 95.67 % Rotamer: Outliers : 0.26 % Allowed : 0.35 % Favored : 99.39 % Cbeta Deviations : 0.08 % 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: 0.86 (0.24), residues: 1249 helix: 1.84 (0.21), residues: 599 sheet: -0.82 (0.43), residues: 132 loop : -0.51 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 740 TYR 0.041 0.002 TYR A 904 PHE 0.028 0.002 PHE A1039 TRP 0.011 0.001 TRP A 590 HIS 0.004 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00384 (10605) covalent geometry : angle 0.64001 (14298) hydrogen bonds : bond 0.12854 ( 527) hydrogen bonds : angle 5.23607 ( 1524) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 183 time to evaluate : 0.368 Fit side-chains revert: symmetry clash REVERT: A 588 LYS cc_start: 0.7741 (tmmt) cc_final: 0.7360 (ttpt) REVERT: A 593 ILE cc_start: 0.8493 (pt) cc_final: 0.8290 (pt) REVERT: A 683 ARG cc_start: 0.7134 (ttm110) cc_final: 0.6763 (ttm-80) REVERT: A 932 ILE cc_start: 0.6124 (mm) cc_final: 0.5744 (mm) REVERT: A 1043 MET cc_start: 0.6535 (mtm) cc_final: 0.6305 (mtp) REVERT: B 430 LYS cc_start: 0.7360 (pttm) cc_final: 0.7113 (ptpp) REVERT: B 600 ASN cc_start: 0.4507 (t0) cc_final: 0.4226 (t0) outliers start: 3 outliers final: 1 residues processed: 185 average time/residue: 0.0903 time to fit residues: 23.6836 Evaluate side-chains 148 residues out of total 1159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 147 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 872 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 10.0000 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.4980 chunk 123 optimal weight: 20.0000 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 HIS A 380 ASN A 677 ASN ** A 825 GLN ** 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 = 0.4580 r_free = 0.4580 target = 0.220326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.193227 restraints weight = 21607.700| |-----------------------------------------------------------------------------| r_work (start): 0.4340 rms_B_bonded: 3.09 r_work (final): 0.4340 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4340 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4340 r_free = 0.4340 target_work(ls_wunit_k1) = 0.193 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4340 r_free = 0.4340 target_work(ls_wunit_k1) = 0.193 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4340 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6342 moved from start: 0.0888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10605 Z= 0.143 Angle : 0.601 7.402 14298 Z= 0.316 Chirality : 0.043 0.264 1544 Planarity : 0.005 0.051 1843 Dihedral : 4.646 26.769 1384 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.61 % Allowed : 7.01 % Favored : 92.39 % 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: 0.96 (0.24), residues: 1249 helix: 1.86 (0.21), residues: 602 sheet: -0.42 (0.44), residues: 123 loop : -0.52 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1047 TYR 0.031 0.002 TYR A 904 PHE 0.031 0.002 PHE A 744 TRP 0.013 0.001 TRP A 552 HIS 0.006 0.001 HIS A 940 Details of bonding type rmsd covalent geometry : bond 0.00331 (10605) covalent geometry : angle 0.60055 (14298) hydrogen bonds : bond 0.04383 ( 527) hydrogen bonds : angle 4.40592 ( 1524) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 161 time to evaluate : 0.374 Fit side-chains REVERT: A 588 LYS cc_start: 0.7751 (tmmt) cc_final: 0.7461 (ttpt) REVERT: A 593 ILE cc_start: 0.8369 (pt) cc_final: 0.8131 (pt) REVERT: A 683 ARG cc_start: 0.6833 (ttm110) cc_final: 0.6504 (ttm-80) REVERT: B 430 LYS cc_start: 0.6952 (pttm) cc_final: 0.6492 (ttpt) outliers start: 7 outliers final: 7 residues processed: 164 average time/residue: 0.0922 time to fit residues: 21.3711 Evaluate side-chains 155 residues out of total 1159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 148 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 677 ASN Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 539 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 63 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 88 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 45 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 chunk 98 optimal weight: 7.9990 chunk 16 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 ASN A 428 ASN A 738 GLN ** A 759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 825 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 931 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1033 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.214856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.176375 restraints weight = 13308.486| |-----------------------------------------------------------------------------| r_work (start): 0.4190 rms_B_bonded: 2.58 r_work (final): 0.4190 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4190 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4190 r_free = 0.4190 target_work(ls_wunit_k1) = 0.177 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4190 r_free = 0.4190 target_work(ls_wunit_k1) = 0.177 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4190 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6571 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 10605 Z= 0.188 Angle : 0.618 7.077 14298 Z= 0.324 Chirality : 0.044 0.234 1544 Planarity : 0.005 0.049 1843 Dihedral : 4.697 20.650 1382 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.12 % Allowed : 10.03 % Favored : 88.84 % 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: 0.83 (0.24), residues: 1249 helix: 1.74 (0.21), residues: 601 sheet: -0.48 (0.44), residues: 126 loop : -0.55 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 741 TYR 0.040 0.002 TYR A 904 PHE 0.021 0.002 PHE A 744 TRP 0.013 0.002 TRP A 590 HIS 0.006 0.001 HIS A 940 Details of bonding type rmsd covalent geometry : bond 0.00453 (10605) covalent geometry : angle 0.61782 (14298) hydrogen bonds : bond 0.04600 ( 527) hydrogen bonds : angle 4.41256 ( 1524) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 152 time to evaluate : 0.265 Fit side-chains REVERT: A 588 LYS cc_start: 0.7719 (tmmt) cc_final: 0.7456 (ttpt) REVERT: B 430 LYS cc_start: 0.7046 (pttm) cc_final: 0.6412 (ttpt) outliers start: 13 outliers final: 12 residues processed: 157 average time/residue: 0.0928 time to fit residues: 20.6602 Evaluate side-chains 155 residues out of total 1159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 143 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 260 TYR Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 539 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 100 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 119 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 41 optimal weight: 0.0970 chunk 109 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 ASN ** A 825 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 931 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.218548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.190394 restraints weight = 21634.942| |-----------------------------------------------------------------------------| r_work (start): 0.4319 rms_B_bonded: 3.19 r_work (final): 0.4319 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4319 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4319 r_free = 0.4319 target_work(ls_wunit_k1) = 0.190 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4319 r_free = 0.4319 target_work(ls_wunit_k1) = 0.190 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4319 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6369 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10605 Z= 0.137 Angle : 0.566 7.321 14298 Z= 0.299 Chirality : 0.041 0.200 1544 Planarity : 0.004 0.050 1843 Dihedral : 4.545 18.879 1382 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.12 % Allowed : 11.16 % Favored : 87.72 % 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: 1.02 (0.24), residues: 1249 helix: 1.89 (0.21), residues: 602 sheet: -0.38 (0.43), residues: 131 loop : -0.44 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 741 TYR 0.037 0.001 TYR A 904 PHE 0.031 0.002 PHE A 734 TRP 0.013 0.001 TRP A 552 HIS 0.005 0.001 HIS A 940 Details of bonding type rmsd covalent geometry : bond 0.00318 (10605) covalent geometry : angle 0.56639 (14298) hydrogen bonds : bond 0.04154 ( 527) hydrogen bonds : angle 4.19672 ( 1524) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 145 time to evaluate : 0.248 Fit side-chains REVERT: A 588 LYS cc_start: 0.7792 (tmmt) cc_final: 0.7560 (ttpt) REVERT: A 593 ILE cc_start: 0.8449 (pt) cc_final: 0.8191 (pt) REVERT: A 679 THR cc_start: 0.7616 (OUTLIER) cc_final: 0.7264 (p) REVERT: B 430 LYS cc_start: 0.6807 (pttm) cc_final: 0.6266 (ttpt) outliers start: 13 outliers final: 9 residues processed: 150 average time/residue: 0.0860 time to fit residues: 18.5202 Evaluate side-chains 150 residues out of total 1159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 140 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 260 TYR Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 539 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 70 optimal weight: 2.9990 chunk 111 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 4 optimal weight: 0.0970 chunk 47 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 49 optimal weight: 3.9990 chunk 119 optimal weight: 6.9990 chunk 22 optimal weight: 0.8980 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 677 ASN ** A 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 803 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.213424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.177730 restraints weight = 17155.701| |-----------------------------------------------------------------------------| r_work (start): 0.4156 rms_B_bonded: 3.31 r_work (final): 0.4156 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4156 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4156 r_free = 0.4156 target_work(ls_wunit_k1) = 0.174 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4156 r_free = 0.4156 target_work(ls_wunit_k1) = 0.174 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4156 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6607 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 10605 Z= 0.257 Angle : 0.682 7.528 14298 Z= 0.356 Chirality : 0.046 0.219 1544 Planarity : 0.005 0.063 1843 Dihedral : 5.001 22.870 1382 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.73 % Allowed : 12.20 % Favored : 86.07 % 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: 0.50 (0.24), residues: 1249 helix: 1.49 (0.21), residues: 598 sheet: -0.83 (0.42), residues: 139 loop : -0.66 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 741 TYR 0.049 0.003 TYR A 904 PHE 0.029 0.003 PHE A 734 TRP 0.018 0.002 TRP A 590 HIS 0.008 0.001 HIS A 855 Details of bonding type rmsd covalent geometry : bond 0.00624 (10605) covalent geometry : angle 0.68173 (14298) hydrogen bonds : bond 0.05050 ( 527) hydrogen bonds : angle 4.55477 ( 1524) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 147 time to evaluate : 0.274 Fit side-chains outliers start: 20 outliers final: 16 residues processed: 155 average time/residue: 0.0889 time to fit residues: 19.6313 Evaluate side-chains 157 residues out of total 1159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 141 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 260 TYR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 539 ILE Chi-restraints excluded: chain B residue 540 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 1 optimal weight: 0.4980 chunk 85 optimal weight: 0.9980 chunk 112 optimal weight: 3.9990 chunk 21 optimal weight: 8.9990 chunk 87 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 43 optimal weight: 0.3980 chunk 38 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 124 optimal weight: 20.0000 chunk 40 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 920 ASN ** 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 = 0.4598 r_free = 0.4598 target = 0.222699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.189673 restraints weight = 17606.267| |-----------------------------------------------------------------------------| r_work (start): 0.4235 rms_B_bonded: 3.20 r_work (final): 0.4235 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4235 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4235 r_free = 0.4235 target_work(ls_wunit_k1) = 0.181 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4235 r_free = 0.4235 target_work(ls_wunit_k1) = 0.181 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4235 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6491 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10605 Z= 0.151 Angle : 0.580 7.349 14298 Z= 0.306 Chirality : 0.042 0.317 1544 Planarity : 0.005 0.074 1843 Dihedral : 4.729 19.286 1382 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.56 % Allowed : 12.98 % Favored : 85.47 % 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: 0.78 (0.24), residues: 1249 helix: 1.71 (0.21), residues: 600 sheet: -0.70 (0.43), residues: 126 loop : -0.54 (0.28), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 465 TYR 0.046 0.002 TYR A 904 PHE 0.033 0.002 PHE A 734 TRP 0.014 0.002 TRP A 552 HIS 0.005 0.001 HIS A 940 Details of bonding type rmsd covalent geometry : bond 0.00359 (10605) covalent geometry : angle 0.57980 (14298) hydrogen bonds : bond 0.04294 ( 527) hydrogen bonds : angle 4.24462 ( 1524) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 148 time to evaluate : 0.409 Fit side-chains REVERT: A 794 PHE cc_start: 0.5934 (p90) cc_final: 0.5626 (p90) REVERT: B 430 LYS cc_start: 0.6868 (pttm) cc_final: 0.6286 (ttpt) REVERT: B 582 MET cc_start: 0.6165 (mtp) cc_final: 0.5721 (ptp) outliers start: 18 outliers final: 15 residues processed: 157 average time/residue: 0.0917 time to fit residues: 21.0639 Evaluate side-chains 157 residues out of total 1159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 142 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 260 TYR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 539 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 115 optimal weight: 10.0000 chunk 113 optimal weight: 0.9990 chunk 123 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 54 optimal weight: 0.1980 chunk 46 optimal weight: 0.0570 chunk 106 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 65 optimal weight: 0.3980 chunk 110 optimal weight: 10.0000 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 579 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.219225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.182168 restraints weight = 12989.275| |-----------------------------------------------------------------------------| r_work (start): 0.4248 rms_B_bonded: 2.39 r_work (final): 0.4248 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4248 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4248 r_free = 0.4248 target_work(ls_wunit_k1) = 0.183 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4248 r_free = 0.4248 target_work(ls_wunit_k1) = 0.183 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4248 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6488 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10605 Z= 0.122 Angle : 0.547 7.057 14298 Z= 0.289 Chirality : 0.041 0.342 1544 Planarity : 0.004 0.051 1843 Dihedral : 4.491 18.784 1382 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.30 % Allowed : 13.75 % Favored : 84.95 % 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: 1.07 (0.24), residues: 1249 helix: 1.95 (0.21), residues: 599 sheet: -0.48 (0.42), residues: 131 loop : -0.41 (0.28), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 740 TYR 0.038 0.001 TYR A 904 PHE 0.033 0.002 PHE A 734 TRP 0.014 0.001 TRP A 669 HIS 0.005 0.001 HIS A 940 Details of bonding type rmsd covalent geometry : bond 0.00282 (10605) covalent geometry : angle 0.54684 (14298) hydrogen bonds : bond 0.03907 ( 527) hydrogen bonds : angle 4.04930 ( 1524) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 148 time to evaluate : 0.406 Fit side-chains REVERT: A 593 ILE cc_start: 0.8370 (pt) cc_final: 0.8153 (pt) REVERT: A 679 THR cc_start: 0.7643 (OUTLIER) cc_final: 0.7210 (p) REVERT: A 697 MET cc_start: 0.7713 (tpp) cc_final: 0.6748 (tpp) REVERT: B 430 LYS cc_start: 0.6794 (pttm) cc_final: 0.6259 (ttpt) REVERT: B 582 MET cc_start: 0.6290 (mtp) cc_final: 0.5826 (ptp) outliers start: 15 outliers final: 11 residues processed: 157 average time/residue: 0.1009 time to fit residues: 22.7220 Evaluate side-chains 155 residues out of total 1159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 143 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 579 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 42 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 chunk 124 optimal weight: 20.0000 chunk 58 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 89 optimal weight: 7.9990 chunk 49 optimal weight: 0.9980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1042 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.214392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.187343 restraints weight = 18176.177| |-----------------------------------------------------------------------------| r_work (start): 0.4260 rms_B_bonded: 2.74 r_work (final): 0.4260 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4260 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4260 r_free = 0.4260 target_work(ls_wunit_k1) = 0.185 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4260 r_free = 0.4260 target_work(ls_wunit_k1) = 0.185 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4260 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6466 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 10605 Z= 0.218 Angle : 0.642 7.193 14298 Z= 0.337 Chirality : 0.045 0.442 1544 Planarity : 0.005 0.065 1843 Dihedral : 4.848 20.375 1382 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.38 % Allowed : 14.27 % Favored : 84.34 % 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: 0.67 (0.24), residues: 1249 helix: 1.61 (0.21), residues: 598 sheet: -0.65 (0.42), residues: 141 loop : -0.59 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 740 TYR 0.045 0.002 TYR A 904 PHE 0.034 0.003 PHE A 734 TRP 0.015 0.002 TRP A 590 HIS 0.005 0.001 HIS A 759 Details of bonding type rmsd covalent geometry : bond 0.00529 (10605) covalent geometry : angle 0.64156 (14298) hydrogen bonds : bond 0.04736 ( 527) hydrogen bonds : angle 4.37447 ( 1524) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 151 time to evaluate : 0.430 Fit side-chains REVERT: A 789 MET cc_start: 0.7650 (mtt) cc_final: 0.7115 (mtm) REVERT: B 430 LYS cc_start: 0.6900 (pttm) cc_final: 0.6429 (ttpt) outliers start: 16 outliers final: 14 residues processed: 159 average time/residue: 0.0932 time to fit residues: 21.3606 Evaluate side-chains 161 residues out of total 1159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 147 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 539 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 12 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 101 optimal weight: 8.9990 chunk 56 optimal weight: 0.8980 chunk 103 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 90 optimal weight: 4.9990 chunk 67 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 0.3980 chunk 24 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 ASN ** 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 = 0.4560 r_free = 0.4560 target = 0.218811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.184369 restraints weight = 14648.468| |-----------------------------------------------------------------------------| r_work (start): 0.4228 rms_B_bonded: 2.74 r_work (final): 0.4228 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4228 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4228 r_free = 0.4228 target_work(ls_wunit_k1) = 0.181 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4228 r_free = 0.4228 target_work(ls_wunit_k1) = 0.181 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4228 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6489 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10605 Z= 0.136 Angle : 0.576 7.395 14298 Z= 0.304 Chirality : 0.042 0.408 1544 Planarity : 0.005 0.051 1843 Dihedral : 4.648 19.123 1382 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.12 % Allowed : 14.53 % Favored : 84.34 % 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: 0.93 (0.24), residues: 1249 helix: 1.81 (0.21), residues: 599 sheet: -0.59 (0.42), residues: 135 loop : -0.42 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 740 TYR 0.040 0.001 TYR A 904 PHE 0.034 0.002 PHE A 734 TRP 0.014 0.002 TRP A 783 HIS 0.005 0.001 HIS A 931 Details of bonding type rmsd covalent geometry : bond 0.00321 (10605) covalent geometry : angle 0.57580 (14298) hydrogen bonds : bond 0.04099 ( 527) hydrogen bonds : angle 4.14739 ( 1524) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 149 time to evaluate : 0.396 Fit side-chains REVERT: A 418 GLU cc_start: 0.6025 (tm-30) cc_final: 0.5280 (tt0) REVERT: A 593 ILE cc_start: 0.8370 (pt) cc_final: 0.8123 (pt) REVERT: A 679 THR cc_start: 0.7755 (OUTLIER) cc_final: 0.7334 (p) REVERT: A 789 MET cc_start: 0.7706 (mtt) cc_final: 0.6947 (mtm) REVERT: B 430 LYS cc_start: 0.6913 (pttm) cc_final: 0.6404 (ttpt) outliers start: 13 outliers final: 12 residues processed: 155 average time/residue: 0.0994 time to fit residues: 22.3154 Evaluate side-chains 161 residues out of total 1159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 148 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 260 TYR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 434 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 113 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 2 optimal weight: 9.9990 chunk 79 optimal weight: 0.2980 chunk 25 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 100 optimal weight: 7.9990 chunk 115 optimal weight: 8.9990 chunk 6 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1042 GLN ** B 564 ASN ** 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 = 0.4559 r_free = 0.4559 target = 0.218936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.182052 restraints weight = 15752.282| |-----------------------------------------------------------------------------| r_work (start): 0.4215 rms_B_bonded: 3.10 r_work (final): 0.4215 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4215 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4215 r_free = 0.4215 target_work(ls_wunit_k1) = 0.179 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4215 r_free = 0.4215 target_work(ls_wunit_k1) = 0.179 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4215 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6507 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10605 Z= 0.139 Angle : 0.570 7.089 14298 Z= 0.301 Chirality : 0.042 0.395 1544 Planarity : 0.005 0.051 1843 Dihedral : 4.577 18.707 1382 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.30 % Allowed : 14.71 % Favored : 84.00 % 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: 0.99 (0.24), residues: 1249 helix: 1.84 (0.21), residues: 599 sheet: -0.55 (0.42), residues: 135 loop : -0.38 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 465 TYR 0.039 0.001 TYR A 904 PHE 0.035 0.002 PHE A 734 TRP 0.014 0.002 TRP A 783 HIS 0.005 0.001 HIS A 940 Details of bonding type rmsd covalent geometry : bond 0.00328 (10605) covalent geometry : angle 0.57042 (14298) hydrogen bonds : bond 0.04094 ( 527) hydrogen bonds : angle 4.10546 ( 1524) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 148 time to evaluate : 0.449 Fit side-chains REVERT: A 593 ILE cc_start: 0.8363 (pt) cc_final: 0.8124 (pt) REVERT: A 679 THR cc_start: 0.7742 (OUTLIER) cc_final: 0.7309 (p) REVERT: A 741 ARG cc_start: 0.7153 (ttm-80) cc_final: 0.6897 (mmm-85) REVERT: A 789 MET cc_start: 0.7570 (mtt) cc_final: 0.6768 (mtm) REVERT: B 430 LYS cc_start: 0.6940 (pttm) cc_final: 0.6371 (ttpt) REVERT: B 434 ASP cc_start: 0.5150 (OUTLIER) cc_final: 0.4733 (t70) outliers start: 15 outliers final: 13 residues processed: 155 average time/residue: 0.1067 time to fit residues: 23.9683 Evaluate side-chains 159 residues out of total 1159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 260 TYR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 434 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 63 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 97 optimal weight: 9.9990 chunk 35 optimal weight: 0.4980 chunk 101 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 43 optimal weight: 0.4980 chunk 60 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1042 GLN ** B 564 ASN ** 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 = 0.4542 r_free = 0.4542 target = 0.217341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.188375 restraints weight = 18835.968| |-----------------------------------------------------------------------------| r_work (start): 0.4295 rms_B_bonded: 3.04 r_work (final): 0.4295 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4295 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4295 r_free = 0.4295 target_work(ls_wunit_k1) = 0.188 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4295 r_free = 0.4295 target_work(ls_wunit_k1) = 0.188 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4295 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6385 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10605 Z= 0.134 Angle : 0.563 9.512 14298 Z= 0.296 Chirality : 0.042 0.375 1544 Planarity : 0.005 0.060 1843 Dihedral : 4.529 18.626 1382 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.38 % Allowed : 14.97 % Favored : 83.65 % 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: 1.05 (0.24), residues: 1249 helix: 1.90 (0.21), residues: 598 sheet: -0.53 (0.42), residues: 135 loop : -0.33 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 465 TYR 0.040 0.001 TYR A 904 PHE 0.034 0.002 PHE A 734 TRP 0.014 0.001 TRP A 783 HIS 0.004 0.001 HIS A 940 Details of bonding type rmsd covalent geometry : bond 0.00316 (10605) covalent geometry : angle 0.56317 (14298) hydrogen bonds : bond 0.04015 ( 527) hydrogen bonds : angle 4.05809 ( 1524) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4030.13 seconds wall clock time: 69 minutes 14.79 seconds (4154.79 seconds total)