Starting phenix.real_space_refine on Wed Mar 4 15:04:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lrd_23495/03_2026/7lrd_23495.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lrd_23495/03_2026/7lrd_23495.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lrd_23495/03_2026/7lrd_23495.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lrd_23495/03_2026/7lrd_23495.map" model { file = "/net/cci-nas-00/data/ceres_data/7lrd_23495/03_2026/7lrd_23495.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lrd_23495/03_2026/7lrd_23495.cif" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mn 2 7.51 5 Zn 2 6.06 5 Mg 2 5.21 5 S 94 5.16 5 C 9190 2.51 5 N 2418 2.21 5 O 2638 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14346 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 4150 Classifications: {'peptide': 512} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 501} Chain breaks: 2 Chain: "B" Number of atoms: 2998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2998 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 18, 'TRANS': 352} Chain breaks: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 24 Unusual residues: {' MG': 1, ' MN': 1, 'X5M': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2161 SG CYS A 277 78.349 64.701 53.901 1.00 52.28 S ATOM 2434 SG CYS A 311 79.121 63.550 50.334 1.00 41.08 S ATOM 2440 SG CYS A 312 75.876 62.456 52.045 1.00 39.93 S Restraints were copied for chains: C, D Time building chain proxies: 4.45, per 1000 atoms: 0.31 Number of scatterers: 14346 At special positions: 0 Unit cell: (120.119, 94.607, 130.749, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 Mn 2 24.99 S 94 16.00 Mg 2 11.99 O 2638 8.00 N 2418 7.00 C 9190 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: 1.22 Conformation dependent library (CDL) restraints added in 545.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 601 " pdb="ZN ZN A 601 " - pdb=" ND1 HIS A 275 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 277 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 311 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 312 " pdb=" ZN C 601 " pdb="ZN ZN C 601 " - pdb=" ND1 HIS C 275 " pdb="ZN ZN C 601 " - pdb=" SG CYS C 277 " pdb="ZN ZN C 601 " - pdb=" SG CYS C 311 " pdb="ZN ZN C 601 " - pdb=" SG CYS C 312 " Number of angles added : 6 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3352 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 16 sheets defined 55.3% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 24 through 30 Processing helix chain 'A' and resid 33 through 54 Processing helix chain 'A' and resid 69 through 74 Processing helix chain 'A' and resid 76 through 87 Processing helix chain 'A' and resid 89 through 93 removed outlier: 3.753A pdb=" N TYR A 93 " --> pdb=" O PHE A 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 89 through 93' Processing helix chain 'A' and resid 138 through 152 Processing helix chain 'A' and resid 173 through 186 removed outlier: 3.746A pdb=" N MET A 177 " --> pdb=" O GLU A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 233 removed outlier: 4.448A pdb=" N LEU A 215 " --> pdb=" O THR A 211 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLN A 216 " --> pdb=" O GLU A 212 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS A 219 " --> pdb=" O LEU A 215 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU A 220 " --> pdb=" O GLN A 216 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU A 222 " --> pdb=" O ILE A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 253 through 271 removed outlier: 3.515A pdb=" N MET A 271 " --> pdb=" O SER A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 343 Processing helix chain 'A' and resid 392 through 403 Processing helix chain 'A' and resid 403 through 415 removed outlier: 3.979A pdb=" N LYS A 407 " --> pdb=" O HIS A 403 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN A 408 " --> pdb=" O GLU A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 432 removed outlier: 3.632A pdb=" N ASP A 431 " --> pdb=" O SER A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 483 Processing helix chain 'A' and resid 519 through 524 removed outlier: 3.800A pdb=" N PHE A 524 " --> pdb=" O SER A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 541 Processing helix chain 'A' and resid 551 through 559 Processing helix chain 'B' and resid 679 through 683 removed outlier: 3.621A pdb=" N LEU B 682 " --> pdb=" O MET B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 684 through 691 removed outlier: 4.163A pdb=" N ASN B 690 " --> pdb=" O GLU B 687 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR B 691 " --> pdb=" O GLN B 688 " (cutoff:3.500A) Processing helix chain 'B' and resid 695 through 704 Processing helix chain 'B' and resid 709 through 723 Processing helix chain 'B' and resid 723 through 728 Processing helix chain 'B' and resid 731 through 746 Processing helix chain 'B' and resid 753 through 770 Processing helix chain 'B' and resid 816 through 820 Processing helix chain 'B' and resid 822 through 836 Processing helix chain 'B' and resid 844 through 851 Processing helix chain 'B' and resid 853 through 859 Processing helix chain 'B' and resid 863 through 880 removed outlier: 4.033A pdb=" N ARG B 880 " --> pdb=" O LEU B 876 " (cutoff:3.500A) Processing helix chain 'B' and resid 881 through 884 Processing helix chain 'B' and resid 890 through 908 removed outlier: 3.679A pdb=" N THR B 908 " --> pdb=" O ALA B 904 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 926 Processing helix chain 'B' and resid 934 through 951 removed outlier: 3.584A pdb=" N ILE B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 952 through 956 Processing helix chain 'B' and resid 957 through 983 Processing helix chain 'B' and resid 996 through 1008 Processing helix chain 'B' and resid 1008 through 1020 Processing helix chain 'B' and resid 1073 through 1100 Processing helix chain 'C' and resid 24 through 30 Processing helix chain 'C' and resid 33 through 54 Processing helix chain 'C' and resid 69 through 74 Processing helix chain 'C' and resid 76 through 87 Processing helix chain 'C' and resid 89 through 93 removed outlier: 3.754A pdb=" N TYR C 93 " --> pdb=" O PHE C 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 89 through 93' Processing helix chain 'C' and resid 138 through 152 Processing helix chain 'C' and resid 173 through 186 removed outlier: 3.745A pdb=" N MET C 177 " --> pdb=" O GLU C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 233 removed outlier: 4.448A pdb=" N LEU C 215 " --> pdb=" O THR C 211 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLN C 216 " --> pdb=" O GLU C 212 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS C 219 " --> pdb=" O LEU C 215 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU C 220 " --> pdb=" O GLN C 216 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU C 222 " --> pdb=" O ILE C 218 " (cutoff:3.500A) Proline residue: C 223 - end of helix Processing helix chain 'C' and resid 253 through 271 removed outlier: 3.514A pdb=" N MET C 271 " --> pdb=" O SER C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 343 Processing helix chain 'C' and resid 392 through 403 Processing helix chain 'C' and resid 403 through 415 removed outlier: 3.979A pdb=" N LYS C 407 " --> pdb=" O HIS C 403 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN C 408 " --> pdb=" O GLU C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 432 removed outlier: 3.631A pdb=" N ASP C 431 " --> pdb=" O SER C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 483 Processing helix chain 'C' and resid 519 through 524 removed outlier: 3.799A pdb=" N PHE C 524 " --> pdb=" O SER C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 541 Processing helix chain 'C' and resid 551 through 559 Processing helix chain 'D' and resid 679 through 683 removed outlier: 3.620A pdb=" N LEU D 682 " --> pdb=" O MET D 679 " (cutoff:3.500A) Processing helix chain 'D' and resid 684 through 691 removed outlier: 4.163A pdb=" N ASN D 690 " --> pdb=" O GLU D 687 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR D 691 " --> pdb=" O GLN D 688 " (cutoff:3.500A) Processing helix chain 'D' and resid 695 through 704 Processing helix chain 'D' and resid 709 through 723 Processing helix chain 'D' and resid 723 through 728 Processing helix chain 'D' and resid 731 through 746 Processing helix chain 'D' and resid 753 through 770 Processing helix chain 'D' and resid 816 through 820 Processing helix chain 'D' and resid 822 through 836 Processing helix chain 'D' and resid 844 through 851 Processing helix chain 'D' and resid 853 through 859 Processing helix chain 'D' and resid 863 through 880 removed outlier: 4.034A pdb=" N ARG D 880 " --> pdb=" O LEU D 876 " (cutoff:3.500A) Processing helix chain 'D' and resid 881 through 884 Processing helix chain 'D' and resid 890 through 908 removed outlier: 3.679A pdb=" N THR D 908 " --> pdb=" O ALA D 904 " (cutoff:3.500A) Processing helix chain 'D' and resid 912 through 926 Processing helix chain 'D' and resid 934 through 951 removed outlier: 3.586A pdb=" N ILE D 951 " --> pdb=" O LYS D 947 " (cutoff:3.500A) Processing helix chain 'D' and resid 952 through 956 Processing helix chain 'D' and resid 957 through 983 Processing helix chain 'D' and resid 996 through 1008 Processing helix chain 'D' and resid 1008 through 1020 Processing helix chain 'D' and resid 1073 through 1100 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 5 removed outlier: 6.634A pdb=" N VAL A 58 " --> pdb=" O VAL A 15 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N ASP A 17 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LYS A 60 " --> pdb=" O ASP A 17 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLY A 19 " --> pdb=" O LYS A 60 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 127 through 130 Processing sheet with id=AA3, first strand: chain 'A' and resid 171 through 172 removed outlier: 6.633A pdb=" N VAL C 58 " --> pdb=" O VAL C 15 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N ASP C 17 " --> pdb=" O VAL C 58 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LYS C 60 " --> pdb=" O ASP C 17 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLY C 19 " --> pdb=" O LYS C 60 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 189 through 191 removed outlier: 6.663A pdb=" N LEU A 190 " --> pdb=" O TYR A 293 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N SER A 286 " --> pdb=" O LEU A 305 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU A 305 " --> pdb=" O SER A 286 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LYS A 288 " --> pdb=" O CYS A 303 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N CYS A 303 " --> pdb=" O LYS A 288 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU A 290 " --> pdb=" O TYR A 301 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N TYR A 301 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL A 292 " --> pdb=" O CYS A 299 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 273 through 274 Processing sheet with id=AA6, first strand: chain 'A' and resid 322 through 325 Processing sheet with id=AA7, first strand: chain 'A' and resid 388 through 391 removed outlier: 5.802A pdb=" N THR A 389 " --> pdb=" O LEU A 422 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N PHE A 424 " --> pdb=" O THR A 389 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N THR A 391 " --> pdb=" O PHE A 424 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N CYS A 442 " --> pdb=" O PHE A 458 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR A 510 " --> pdb=" O ILE A 497 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N TYR A 499 " --> pdb=" O CYS A 508 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N CYS A 508 " --> pdb=" O TYR A 499 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 772 through 773 Processing sheet with id=AA9, first strand: chain 'B' and resid 1025 through 1027 removed outlier: 3.506A pdb=" N LYS B1070 " --> pdb=" O VAL B1027 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 127 through 130 Processing sheet with id=AB2, first strand: chain 'C' and resid 189 through 191 removed outlier: 6.663A pdb=" N LEU C 190 " --> pdb=" O TYR C 293 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N SER C 286 " --> pdb=" O LEU C 305 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LEU C 305 " --> pdb=" O SER C 286 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LYS C 288 " --> pdb=" O CYS C 303 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N CYS C 303 " --> pdb=" O LYS C 288 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU C 290 " --> pdb=" O TYR C 301 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N TYR C 301 " --> pdb=" O LEU C 290 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL C 292 " --> pdb=" O CYS C 299 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 273 through 274 Processing sheet with id=AB4, first strand: chain 'C' and resid 322 through 325 Processing sheet with id=AB5, first strand: chain 'C' and resid 388 through 391 removed outlier: 5.802A pdb=" N THR C 389 " --> pdb=" O LEU C 422 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N PHE C 424 " --> pdb=" O THR C 389 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N THR C 391 " --> pdb=" O PHE C 424 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N CYS C 442 " --> pdb=" O PHE C 458 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR C 510 " --> pdb=" O ILE C 497 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N TYR C 499 " --> pdb=" O CYS C 508 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N CYS C 508 " --> pdb=" O TYR C 499 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 772 through 773 Processing sheet with id=AB7, first strand: chain 'D' and resid 1025 through 1027 removed outlier: 3.505A pdb=" N LYS D1070 " --> pdb=" O VAL D1027 " (cutoff:3.500A) 768 hydrogen bonds defined for protein. 2172 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: 3.06 Time building geometry restraints manager: 1.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2902 1.33 - 1.45: 3404 1.45 - 1.57: 8190 1.57 - 1.69: 0 1.69 - 1.81: 146 Bond restraints: 14642 Sorted by residual: bond pdb=" N LYS C 150 " pdb=" CA LYS C 150 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.78e+00 bond pdb=" N LYS A 150 " pdb=" CA LYS A 150 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.78e+00 bond pdb=" N PHE C 548 " pdb=" CA PHE C 548 " ideal model delta sigma weight residual 1.456 1.485 -0.028 1.23e-02 6.61e+03 5.19e+00 bond pdb=" N PHE A 548 " pdb=" CA PHE A 548 " ideal model delta sigma weight residual 1.456 1.484 -0.028 1.23e-02 6.61e+03 5.18e+00 bond pdb=" N GLU A 552 " pdb=" CA GLU A 552 " ideal model delta sigma weight residual 1.459 1.484 -0.025 1.21e-02 6.83e+03 4.33e+00 ... (remaining 14637 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 19577 2.15 - 4.31: 147 4.31 - 6.46: 22 6.46 - 8.61: 0 8.61 - 10.77: 2 Bond angle restraints: 19748 Sorted by residual: angle pdb=" C05 X5M B2003 " pdb=" C04 X5M B2003 " pdb=" N03 X5M B2003 " ideal model delta sigma weight residual 115.49 104.72 10.77 3.00e+00 1.11e-01 1.29e+01 angle pdb=" C05 X5M D2003 " pdb=" C04 X5M D2003 " pdb=" N03 X5M D2003 " ideal model delta sigma weight residual 115.49 104.77 10.72 3.00e+00 1.11e-01 1.28e+01 angle pdb=" N ARG A 129 " pdb=" CA ARG A 129 " pdb=" C ARG A 129 " ideal model delta sigma weight residual 107.99 113.54 -5.55 1.77e+00 3.19e-01 9.82e+00 angle pdb=" N ARG C 129 " pdb=" CA ARG C 129 " pdb=" C ARG C 129 " ideal model delta sigma weight residual 107.99 113.51 -5.52 1.77e+00 3.19e-01 9.71e+00 angle pdb=" C GLN C 547 " pdb=" N PHE C 548 " pdb=" CA PHE C 548 " ideal model delta sigma weight residual 122.72 118.43 4.29 1.38e+00 5.25e-01 9.68e+00 ... (remaining 19743 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.68: 8598 16.68 - 33.35: 202 33.35 - 50.03: 34 50.03 - 66.70: 2 66.70 - 83.38: 2 Dihedral angle restraints: 8838 sinusoidal: 3658 harmonic: 5180 Sorted by residual: dihedral pdb=" CB GLU C 205 " pdb=" CG GLU C 205 " pdb=" CD GLU C 205 " pdb=" OE1 GLU C 205 " ideal model delta sinusoidal sigma weight residual 0.00 -83.38 83.38 1 3.00e+01 1.11e-03 9.44e+00 dihedral pdb=" CB GLU A 205 " pdb=" CG GLU A 205 " pdb=" CD GLU A 205 " pdb=" OE1 GLU A 205 " ideal model delta sinusoidal sigma weight residual 0.00 -83.36 83.36 1 3.00e+01 1.11e-03 9.43e+00 dihedral pdb=" CA MET D 835 " pdb=" C MET D 835 " pdb=" N HIS D 836 " pdb=" CA HIS D 836 " ideal model delta harmonic sigma weight residual -180.00 -166.05 -13.95 0 5.00e+00 4.00e-02 7.79e+00 ... (remaining 8835 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1815 0.049 - 0.097: 261 0.097 - 0.146: 82 0.146 - 0.194: 2 0.194 - 0.243: 4 Chirality restraints: 2164 Sorted by residual: chirality pdb=" CB ILE C 131 " pdb=" CA ILE C 131 " pdb=" CG1 ILE C 131 " pdb=" CG2 ILE C 131 " both_signs ideal model delta sigma weight residual False 2.64 2.89 -0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CB ILE A 131 " pdb=" CA ILE A 131 " pdb=" CG1 ILE A 131 " pdb=" CG2 ILE A 131 " both_signs ideal model delta sigma weight residual False 2.64 2.89 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" C21 X5M D2003 " pdb=" C15 X5M D2003 " pdb=" C20 X5M D2003 " pdb=" C22 X5M D2003 " both_signs ideal model delta sigma weight residual False -2.63 -2.84 0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 2161 not shown) Planarity restraints: 2516 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C02 X5M B2003 " 0.057 2.00e-02 2.50e+03 1.00e-01 1.01e+02 pdb=" C04 X5M B2003 " 0.057 2.00e-02 2.50e+03 pdb=" C06 X5M B2003 " 0.060 2.00e-02 2.50e+03 pdb=" N03 X5M B2003 " -0.174 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C02 X5M D2003 " 0.056 2.00e-02 2.50e+03 1.00e-01 1.00e+02 pdb=" C04 X5M D2003 " 0.057 2.00e-02 2.50e+03 pdb=" C06 X5M D2003 " 0.060 2.00e-02 2.50e+03 pdb=" N03 X5M D2003 " -0.174 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C18 X5M D2003 " 0.014 2.00e-02 2.50e+03 5.87e-02 4.31e+01 pdb=" C20 X5M D2003 " 0.016 2.00e-02 2.50e+03 pdb=" N16 X5M D2003 " -0.070 2.00e-02 2.50e+03 pdb=" N17 X5M D2003 " 0.095 2.00e-02 2.50e+03 pdb=" O19 X5M D2003 " -0.055 2.00e-02 2.50e+03 ... (remaining 2513 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 38 2.42 - 3.04: 8881 3.04 - 3.66: 20247 3.66 - 4.28: 33090 4.28 - 4.90: 55726 Nonbonded interactions: 117982 Sorted by model distance: nonbonded pdb=" OD1 ASP B 950 " pdb="MN MN B2001 " model vdw 1.795 2.320 nonbonded pdb=" OD1 ASP D 950 " pdb="MN MN D2001 " model vdw 1.795 2.320 nonbonded pdb=" OD2 ASP D 837 " pdb="MN MN D2001 " model vdw 2.046 2.320 nonbonded pdb=" OD2 ASP B 837 " pdb="MN MN B2001 " model vdw 2.046 2.320 nonbonded pdb=" OD1 ASP D 837 " pdb="MG MG D2002 " model vdw 2.141 2.170 ... (remaining 117977 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.400 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.000 Find NCS groups from input model: 0.080 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 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 : 0.003 0.051 14650 Z= 0.145 Angle : 0.480 10.767 19754 Z= 0.286 Chirality : 0.039 0.243 2164 Planarity : 0.004 0.100 2516 Dihedral : 7.755 83.376 5486 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.25 % Allowed : 1.27 % Favored : 98.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 2.71 (0.20), residues: 1742 helix: 2.82 (0.18), residues: 882 sheet: 1.81 (0.40), residues: 164 loop : 0.49 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 309 TYR 0.012 0.001 TYR B 738 PHE 0.012 0.001 PHE C 548 TRP 0.008 0.001 TRP B 874 HIS 0.002 0.000 HIS B 869 Details of bonding type rmsd covalent geometry : bond 0.00261 (14642) covalent geometry : angle 0.47946 (19748) hydrogen bonds : bond 0.12633 ( 768) hydrogen bonds : angle 4.38488 ( 2172) metal coordination : bond 0.00350 ( 8) metal coordination : angle 0.86230 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 112 time to evaluate : 0.544 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 116 average time/residue: 0.1390 time to fit residues: 23.2185 Evaluate side-chains 72 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 68 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 HIS Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain D residue 710 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 HIS B 999 ASN B1007 HIS B1074 GLN C 274 HIS D 999 ASN D1007 HIS D1074 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.045403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.034579 restraints weight = 76478.768| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 3.92 r_work: 0.2664 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 14650 Z= 0.291 Angle : 0.583 6.763 19754 Z= 0.301 Chirality : 0.040 0.143 2164 Planarity : 0.004 0.046 2516 Dihedral : 4.378 37.858 1946 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.64 % Allowed : 4.26 % Favored : 95.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 2.62 (0.20), residues: 1742 helix: 2.77 (0.18), residues: 882 sheet: 1.81 (0.38), residues: 164 loop : 0.41 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 328 TYR 0.014 0.002 TYR A 555 PHE 0.020 0.002 PHE A 145 TRP 0.007 0.001 TRP B 932 HIS 0.008 0.001 HIS D 868 Details of bonding type rmsd covalent geometry : bond 0.00633 (14642) covalent geometry : angle 0.58143 (19748) hydrogen bonds : bond 0.03522 ( 768) hydrogen bonds : angle 3.90859 ( 2172) metal coordination : bond 0.02661 ( 8) metal coordination : angle 2.18432 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.592 Fit side-chains revert: symmetry clash REVERT: A 460 MET cc_start: 0.9182 (mmm) cc_final: 0.8964 (mmp) REVERT: B 1022 MET cc_start: 0.9004 (tpp) cc_final: 0.8610 (tmm) REVERT: D 1022 MET cc_start: 0.9012 (tpp) cc_final: 0.8621 (tmm) outliers start: 10 outliers final: 4 residues processed: 76 average time/residue: 0.0927 time to fit residues: 12.0430 Evaluate side-chains 66 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 HIS Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain D residue 710 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 16 optimal weight: 0.9990 chunk 62 optimal weight: 9.9990 chunk 152 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 103 optimal weight: 0.3980 chunk 80 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 66 optimal weight: 0.0030 chunk 165 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.046503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.035641 restraints weight = 75104.947| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 3.99 r_work: 0.2703 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 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 : 0.002 0.028 14650 Z= 0.093 Angle : 0.427 6.712 19754 Z= 0.223 Chirality : 0.037 0.136 2164 Planarity : 0.003 0.043 2516 Dihedral : 4.128 40.798 1946 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.64 % Allowed : 4.01 % Favored : 95.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 2.81 (0.20), residues: 1742 helix: 2.97 (0.18), residues: 880 sheet: 1.87 (0.39), residues: 162 loop : 0.45 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 328 TYR 0.009 0.001 TYR B 766 PHE 0.016 0.001 PHE A 145 TRP 0.005 0.001 TRP B 932 HIS 0.002 0.000 HIS A 403 Details of bonding type rmsd covalent geometry : bond 0.00205 (14642) covalent geometry : angle 0.42528 (19748) hydrogen bonds : bond 0.02789 ( 768) hydrogen bonds : angle 3.57083 ( 2172) metal coordination : bond 0.00567 ( 8) metal coordination : angle 2.13559 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.560 Fit side-chains REVERT: A 177 MET cc_start: 0.9065 (OUTLIER) cc_final: 0.8679 (tpp) REVERT: A 414 MET cc_start: 0.8954 (mmm) cc_final: 0.8712 (mmm) REVERT: A 460 MET cc_start: 0.9162 (mmm) cc_final: 0.8923 (mmp) REVERT: B 722 MET cc_start: 0.9133 (mmm) cc_final: 0.8805 (mmm) REVERT: B 990 MET cc_start: 0.8543 (mtm) cc_final: 0.8000 (mtp) REVERT: B 1022 MET cc_start: 0.8905 (tpp) cc_final: 0.8558 (tmm) REVERT: B 1085 MET cc_start: 0.9104 (tmm) cc_final: 0.8806 (tmm) REVERT: C 177 MET cc_start: 0.9078 (OUTLIER) cc_final: 0.8689 (tpp) REVERT: C 414 MET cc_start: 0.8973 (mmm) cc_final: 0.8735 (mmm) REVERT: C 460 MET cc_start: 0.9316 (mmm) cc_final: 0.8889 (mmm) REVERT: D 722 MET cc_start: 0.9130 (mmm) cc_final: 0.8803 (mmm) REVERT: D 990 MET cc_start: 0.8534 (mtm) cc_final: 0.7998 (mtp) REVERT: D 1022 MET cc_start: 0.8925 (tpp) cc_final: 0.8582 (tmm) REVERT: D 1085 MET cc_start: 0.9106 (tmm) cc_final: 0.8808 (tmm) outliers start: 10 outliers final: 4 residues processed: 72 average time/residue: 0.0987 time to fit residues: 11.9484 Evaluate side-chains 68 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 323 HIS Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain D residue 710 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 133 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 154 optimal weight: 0.0370 chunk 41 optimal weight: 7.9990 chunk 14 optimal weight: 0.8980 chunk 164 optimal weight: 1.9990 chunk 138 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 66 optimal weight: 8.9990 overall best weight: 2.7864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 752 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 = 0.3209 r_free = 0.3209 target = 0.044744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.033891 restraints weight = 77381.236| |-----------------------------------------------------------------------------| r_work (start): 0.2785 rms_B_bonded: 3.97 r_work: 0.2635 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14650 Z= 0.244 Angle : 0.538 7.498 19754 Z= 0.278 Chirality : 0.039 0.140 2164 Planarity : 0.004 0.043 2516 Dihedral : 4.333 41.678 1946 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.95 % Favored : 97.93 % Rotamer: Outliers : 0.32 % Allowed : 4.64 % Favored : 95.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 2.63 (0.20), residues: 1742 helix: 2.84 (0.17), residues: 880 sheet: 1.78 (0.38), residues: 162 loop : 0.34 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 526 TYR 0.013 0.002 TYR C 529 PHE 0.017 0.001 PHE A 145 TRP 0.007 0.001 TRP D 874 HIS 0.008 0.001 HIS D 868 Details of bonding type rmsd covalent geometry : bond 0.00527 (14642) covalent geometry : angle 0.53702 (19748) hydrogen bonds : bond 0.03276 ( 768) hydrogen bonds : angle 3.77515 ( 2172) metal coordination : bond 0.02481 ( 8) metal coordination : angle 1.81334 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.590 Fit side-chains revert: symmetry clash REVERT: A 414 MET cc_start: 0.9193 (mmm) cc_final: 0.8848 (mmm) REVERT: A 460 MET cc_start: 0.9112 (mmm) cc_final: 0.8824 (mmp) REVERT: A 494 MET cc_start: 0.9231 (mmm) cc_final: 0.9015 (mmm) REVERT: B 990 MET cc_start: 0.8747 (mtm) cc_final: 0.8269 (mtp) REVERT: B 1022 MET cc_start: 0.9032 (tpp) cc_final: 0.8638 (tmm) REVERT: B 1085 MET cc_start: 0.9113 (tmm) cc_final: 0.8683 (tmm) REVERT: C 414 MET cc_start: 0.9197 (mmm) cc_final: 0.8862 (mmm) REVERT: C 494 MET cc_start: 0.9245 (mmm) cc_final: 0.9028 (mmm) REVERT: D 990 MET cc_start: 0.8722 (mtm) cc_final: 0.8245 (mtp) REVERT: D 1022 MET cc_start: 0.9040 (tpp) cc_final: 0.8643 (tmm) REVERT: D 1085 MET cc_start: 0.9105 (tmm) cc_final: 0.8675 (tmm) outliers start: 5 outliers final: 4 residues processed: 68 average time/residue: 0.1021 time to fit residues: 11.6914 Evaluate side-chains 66 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 HIS Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain D residue 710 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 62 optimal weight: 9.9990 chunk 52 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 29 optimal weight: 9.9990 chunk 64 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 138 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 145 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 752 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 = 0.3178 r_free = 0.3178 target = 0.043843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.033083 restraints weight = 78472.618| |-----------------------------------------------------------------------------| r_work (start): 0.2756 rms_B_bonded: 3.93 r_work: 0.2603 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.061 14650 Z= 0.356 Angle : 0.613 8.409 19754 Z= 0.318 Chirality : 0.041 0.162 2164 Planarity : 0.004 0.045 2516 Dihedral : 4.594 41.826 1946 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.18 % Favored : 97.70 % Rotamer: Outliers : 0.76 % Allowed : 4.71 % Favored : 94.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 2.16 (0.20), residues: 1742 helix: 2.46 (0.17), residues: 882 sheet: 1.36 (0.38), residues: 164 loop : 0.15 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 526 TYR 0.017 0.002 TYR A 529 PHE 0.019 0.002 PHE A 145 TRP 0.007 0.001 TRP B 932 HIS 0.008 0.002 HIS B 868 Details of bonding type rmsd covalent geometry : bond 0.00767 (14642) covalent geometry : angle 0.61237 (19748) hydrogen bonds : bond 0.03579 ( 768) hydrogen bonds : angle 4.02981 ( 2172) metal coordination : bond 0.03288 ( 8) metal coordination : angle 2.15364 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.592 Fit side-chains revert: symmetry clash REVERT: A 414 MET cc_start: 0.9248 (mmm) cc_final: 0.8833 (mmm) REVERT: A 460 MET cc_start: 0.9089 (mmm) cc_final: 0.8781 (mmp) REVERT: A 494 MET cc_start: 0.9284 (mmm) cc_final: 0.9038 (mmm) REVERT: B 738 TYR cc_start: 0.9433 (t80) cc_final: 0.9224 (t80) REVERT: B 990 MET cc_start: 0.8835 (mtm) cc_final: 0.8368 (mtp) REVERT: B 1022 MET cc_start: 0.9095 (tpp) cc_final: 0.8667 (tmm) REVERT: B 1085 MET cc_start: 0.9116 (tmm) cc_final: 0.8702 (tmm) REVERT: C 414 MET cc_start: 0.9226 (mmm) cc_final: 0.8797 (mmm) REVERT: C 494 MET cc_start: 0.9287 (mmm) cc_final: 0.9040 (mmm) REVERT: D 738 TYR cc_start: 0.9431 (t80) cc_final: 0.9223 (t80) REVERT: D 990 MET cc_start: 0.8832 (mtm) cc_final: 0.8365 (mtp) REVERT: D 1022 MET cc_start: 0.9097 (tpp) cc_final: 0.8671 (tmm) REVERT: D 1085 MET cc_start: 0.9105 (tmm) cc_final: 0.8690 (tmm) outliers start: 12 outliers final: 8 residues processed: 71 average time/residue: 0.0988 time to fit residues: 11.9496 Evaluate side-chains 71 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 323 HIS Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain D residue 710 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 7 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 171 optimal weight: 0.9990 chunk 131 optimal weight: 2.9990 chunk 139 optimal weight: 0.0670 overall best weight: 0.7722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 820 ASN D 820 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.045483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.034676 restraints weight = 76307.330| |-----------------------------------------------------------------------------| r_work (start): 0.2812 rms_B_bonded: 3.99 r_work: 0.2655 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14650 Z= 0.098 Angle : 0.448 9.352 19754 Z= 0.231 Chirality : 0.037 0.132 2164 Planarity : 0.003 0.039 2516 Dihedral : 4.219 43.611 1946 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.84 % Favored : 98.05 % Rotamer: Outliers : 0.64 % Allowed : 4.77 % Favored : 94.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 2.53 (0.20), residues: 1742 helix: 2.80 (0.17), residues: 878 sheet: 1.46 (0.39), residues: 162 loop : 0.32 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 155 TYR 0.007 0.001 TYR D 766 PHE 0.015 0.001 PHE A 145 TRP 0.007 0.001 TRP B 932 HIS 0.002 0.000 HIS A 403 Details of bonding type rmsd covalent geometry : bond 0.00216 (14642) covalent geometry : angle 0.44650 (19748) hydrogen bonds : bond 0.02801 ( 768) hydrogen bonds : angle 3.62401 ( 2172) metal coordination : bond 0.00775 ( 8) metal coordination : angle 1.77641 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.706 Fit side-chains revert: symmetry clash REVERT: A 414 MET cc_start: 0.9149 (mmm) cc_final: 0.8774 (mmm) REVERT: A 460 MET cc_start: 0.9113 (mmm) cc_final: 0.8723 (mmp) REVERT: B 990 MET cc_start: 0.8669 (mtm) cc_final: 0.8135 (mtp) REVERT: B 1022 MET cc_start: 0.9038 (tpp) cc_final: 0.8613 (tmm) REVERT: B 1085 MET cc_start: 0.9146 (tmm) cc_final: 0.8705 (tmm) REVERT: C 414 MET cc_start: 0.9154 (mmm) cc_final: 0.8788 (mmm) REVERT: D 990 MET cc_start: 0.8655 (mtm) cc_final: 0.8130 (mtp) REVERT: D 1022 MET cc_start: 0.9040 (tpp) cc_final: 0.8610 (tmm) REVERT: D 1085 MET cc_start: 0.9135 (tmm) cc_final: 0.8694 (tmm) outliers start: 10 outliers final: 8 residues processed: 74 average time/residue: 0.0912 time to fit residues: 11.4734 Evaluate side-chains 68 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 323 HIS Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain D residue 710 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 142 optimal weight: 9.9990 chunk 42 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 chunk 165 optimal weight: 10.0000 chunk 5 optimal weight: 0.7980 chunk 116 optimal weight: 0.7980 chunk 85 optimal weight: 9.9990 chunk 90 optimal weight: 5.9990 chunk 133 optimal weight: 3.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 943 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.044624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.033894 restraints weight = 77268.931| |-----------------------------------------------------------------------------| r_work (start): 0.2783 rms_B_bonded: 3.96 r_work: 0.2629 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14650 Z= 0.195 Angle : 0.479 6.820 19754 Z= 0.250 Chirality : 0.038 0.137 2164 Planarity : 0.003 0.040 2516 Dihedral : 4.257 44.073 1946 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.18 % Favored : 97.70 % Rotamer: Outliers : 0.76 % Allowed : 4.83 % Favored : 94.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 2.52 (0.20), residues: 1742 helix: 2.83 (0.17), residues: 878 sheet: 1.39 (0.38), residues: 162 loop : 0.27 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 717 TYR 0.011 0.001 TYR C 529 PHE 0.017 0.001 PHE A 145 TRP 0.006 0.001 TRP B 932 HIS 0.005 0.001 HIS B 868 Details of bonding type rmsd covalent geometry : bond 0.00423 (14642) covalent geometry : angle 0.47896 (19748) hydrogen bonds : bond 0.02940 ( 768) hydrogen bonds : angle 3.71914 ( 2172) metal coordination : bond 0.01976 ( 8) metal coordination : angle 1.33432 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.423 Fit side-chains revert: symmetry clash REVERT: A 414 MET cc_start: 0.9209 (mmm) cc_final: 0.8812 (mmm) REVERT: A 460 MET cc_start: 0.9084 (mmm) cc_final: 0.8820 (mmp) REVERT: B 990 MET cc_start: 0.8705 (mtm) cc_final: 0.8173 (mtp) REVERT: B 1022 MET cc_start: 0.9027 (tpp) cc_final: 0.8604 (tmm) REVERT: B 1085 MET cc_start: 0.9147 (tmm) cc_final: 0.8696 (tmm) REVERT: C 414 MET cc_start: 0.9206 (mmm) cc_final: 0.8819 (mmm) REVERT: D 990 MET cc_start: 0.8678 (mtm) cc_final: 0.8143 (mtp) REVERT: D 1022 MET cc_start: 0.9039 (tpp) cc_final: 0.8617 (tmm) REVERT: D 1085 MET cc_start: 0.9135 (tmm) cc_final: 0.8683 (tmm) outliers start: 12 outliers final: 8 residues processed: 71 average time/residue: 0.0907 time to fit residues: 10.8145 Evaluate side-chains 70 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 323 HIS Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain D residue 710 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 84 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 106 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 128 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 159 optimal weight: 0.8980 chunk 17 optimal weight: 5.9990 chunk 160 optimal weight: 0.6980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.045050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.034201 restraints weight = 76945.733| |-----------------------------------------------------------------------------| r_work (start): 0.2797 rms_B_bonded: 3.97 r_work: 0.2646 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14650 Z= 0.152 Angle : 0.468 9.570 19754 Z= 0.243 Chirality : 0.038 0.134 2164 Planarity : 0.003 0.039 2516 Dihedral : 4.216 44.001 1946 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.18 % Favored : 97.70 % Rotamer: Outliers : 0.64 % Allowed : 5.03 % Favored : 94.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 2.54 (0.20), residues: 1742 helix: 2.82 (0.17), residues: 878 sheet: 1.41 (0.38), residues: 162 loop : 0.31 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 155 TYR 0.016 0.001 TYR D 738 PHE 0.017 0.001 PHE A 145 TRP 0.007 0.001 TRP D 932 HIS 0.004 0.001 HIS B 868 Details of bonding type rmsd covalent geometry : bond 0.00334 (14642) covalent geometry : angle 0.46720 (19748) hydrogen bonds : bond 0.02818 ( 768) hydrogen bonds : angle 3.65371 ( 2172) metal coordination : bond 0.01425 ( 8) metal coordination : angle 1.48372 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 414 MET cc_start: 0.9197 (mmm) cc_final: 0.8813 (mmm) REVERT: A 460 MET cc_start: 0.9076 (mmm) cc_final: 0.8805 (mmp) REVERT: B 738 TYR cc_start: 0.9383 (t80) cc_final: 0.9069 (t80) REVERT: B 990 MET cc_start: 0.8674 (mtm) cc_final: 0.8119 (mtp) REVERT: B 1022 MET cc_start: 0.8971 (tpp) cc_final: 0.8571 (tmm) REVERT: B 1085 MET cc_start: 0.9147 (tmm) cc_final: 0.8691 (tmm) REVERT: C 414 MET cc_start: 0.9183 (mmm) cc_final: 0.8797 (mmm) REVERT: D 738 TYR cc_start: 0.9381 (t80) cc_final: 0.9070 (t80) REVERT: D 990 MET cc_start: 0.8666 (mtm) cc_final: 0.8110 (mtp) REVERT: D 1022 MET cc_start: 0.8989 (tpp) cc_final: 0.8585 (tmm) REVERT: D 1085 MET cc_start: 0.9128 (tmm) cc_final: 0.8671 (tmm) outliers start: 10 outliers final: 8 residues processed: 69 average time/residue: 0.0937 time to fit residues: 10.9994 Evaluate side-chains 69 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 323 HIS Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain D residue 710 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 92 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 3 optimal weight: 7.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 943 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.044891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.034155 restraints weight = 77459.217| |-----------------------------------------------------------------------------| r_work (start): 0.2794 rms_B_bonded: 3.95 r_work: 0.2643 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14650 Z= 0.173 Angle : 0.484 8.677 19754 Z= 0.249 Chirality : 0.038 0.135 2164 Planarity : 0.003 0.039 2516 Dihedral : 4.240 43.872 1946 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.18 % Favored : 97.70 % Rotamer: Outliers : 0.76 % Allowed : 4.90 % Favored : 94.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 2.53 (0.20), residues: 1742 helix: 2.82 (0.18), residues: 878 sheet: 1.41 (0.38), residues: 162 loop : 0.30 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 155 TYR 0.016 0.001 TYR D 738 PHE 0.018 0.001 PHE C 145 TRP 0.006 0.001 TRP D 932 HIS 0.004 0.001 HIS B 868 Details of bonding type rmsd covalent geometry : bond 0.00380 (14642) covalent geometry : angle 0.48347 (19748) hydrogen bonds : bond 0.02888 ( 768) hydrogen bonds : angle 3.67577 ( 2172) metal coordination : bond 0.01702 ( 8) metal coordination : angle 1.35139 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.607 Fit side-chains revert: symmetry clash REVERT: A 414 MET cc_start: 0.9198 (mmm) cc_final: 0.8803 (mmm) REVERT: A 460 MET cc_start: 0.9052 (mmm) cc_final: 0.8783 (mmp) REVERT: B 990 MET cc_start: 0.8691 (mtm) cc_final: 0.8129 (mtp) REVERT: B 1022 MET cc_start: 0.9004 (tpp) cc_final: 0.8592 (tmm) REVERT: B 1085 MET cc_start: 0.9151 (tmm) cc_final: 0.8692 (tmm) REVERT: C 414 MET cc_start: 0.9204 (mmm) cc_final: 0.8811 (mmm) REVERT: D 990 MET cc_start: 0.8678 (mtm) cc_final: 0.8119 (mtp) REVERT: D 1022 MET cc_start: 0.9019 (tpp) cc_final: 0.8606 (tmm) REVERT: D 1085 MET cc_start: 0.9127 (tmm) cc_final: 0.8668 (tmm) outliers start: 12 outliers final: 8 residues processed: 71 average time/residue: 0.0948 time to fit residues: 11.4477 Evaluate side-chains 69 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 323 HIS Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain D residue 710 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 73 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 149 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 159 optimal weight: 0.9980 chunk 101 optimal weight: 4.9990 chunk 131 optimal weight: 0.8980 chunk 24 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.045026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.034263 restraints weight = 77202.086| |-----------------------------------------------------------------------------| r_work (start): 0.2799 rms_B_bonded: 3.94 r_work: 0.2650 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14650 Z= 0.159 Angle : 0.471 8.498 19754 Z= 0.244 Chirality : 0.038 0.135 2164 Planarity : 0.003 0.038 2516 Dihedral : 4.260 44.010 1946 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.18 % Favored : 97.70 % Rotamer: Outliers : 0.51 % Allowed : 5.34 % Favored : 94.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 2.64 (0.20), residues: 1742 helix: 2.93 (0.18), residues: 866 sheet: 1.41 (0.38), residues: 162 loop : 0.39 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 513 TYR 0.018 0.001 TYR D 738 PHE 0.018 0.001 PHE C 145 TRP 0.006 0.001 TRP D 932 HIS 0.004 0.001 HIS B 868 Details of bonding type rmsd covalent geometry : bond 0.00348 (14642) covalent geometry : angle 0.47010 (19748) hydrogen bonds : bond 0.02848 ( 768) hydrogen bonds : angle 3.64729 ( 2172) metal coordination : bond 0.01509 ( 8) metal coordination : angle 1.40741 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.546 Fit side-chains revert: symmetry clash REVERT: A 414 MET cc_start: 0.9188 (mmm) cc_final: 0.8802 (mmm) REVERT: A 460 MET cc_start: 0.9033 (mmm) cc_final: 0.8745 (mmp) REVERT: B 738 TYR cc_start: 0.9368 (t80) cc_final: 0.8839 (t80) REVERT: B 990 MET cc_start: 0.8711 (mtm) cc_final: 0.8281 (mtp) REVERT: B 1022 MET cc_start: 0.8990 (tpp) cc_final: 0.8583 (tmm) REVERT: B 1085 MET cc_start: 0.9144 (tmm) cc_final: 0.8681 (tmm) REVERT: C 414 MET cc_start: 0.9184 (mmm) cc_final: 0.8792 (mmm) REVERT: D 738 TYR cc_start: 0.9370 (t80) cc_final: 0.8839 (t80) REVERT: D 990 MET cc_start: 0.8688 (mtm) cc_final: 0.8261 (mtp) REVERT: D 1022 MET cc_start: 0.8999 (tpp) cc_final: 0.8593 (tmm) REVERT: D 1085 MET cc_start: 0.9121 (tmm) cc_final: 0.8660 (tmm) outliers start: 8 outliers final: 8 residues processed: 67 average time/residue: 0.0921 time to fit residues: 10.5866 Evaluate side-chains 68 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 323 HIS Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain D residue 710 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 11 optimal weight: 2.9990 chunk 163 optimal weight: 0.5980 chunk 93 optimal weight: 4.9990 chunk 112 optimal weight: 7.9990 chunk 42 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 148 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.045534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.034739 restraints weight = 77298.167| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 3.98 r_work: 0.2667 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 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 : 0.002 0.041 14650 Z= 0.108 Angle : 0.453 11.093 19754 Z= 0.231 Chirality : 0.037 0.134 2164 Planarity : 0.003 0.038 2516 Dihedral : 4.173 44.181 1946 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.95 % Favored : 97.93 % Rotamer: Outliers : 0.51 % Allowed : 5.03 % Favored : 94.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 2.69 (0.20), residues: 1742 helix: 2.93 (0.18), residues: 870 sheet: 1.51 (0.39), residues: 162 loop : 0.42 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 513 TYR 0.018 0.001 TYR D 738 PHE 0.017 0.001 PHE C 145 TRP 0.006 0.001 TRP D 932 HIS 0.002 0.001 HIS B 868 Details of bonding type rmsd covalent geometry : bond 0.00241 (14642) covalent geometry : angle 0.45212 (19748) hydrogen bonds : bond 0.02645 ( 768) hydrogen bonds : angle 3.55555 ( 2172) metal coordination : bond 0.00903 ( 8) metal coordination : angle 1.73292 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2814.58 seconds wall clock time: 49 minutes 9.71 seconds (2949.71 seconds total)