Starting phenix.real_space_refine on Fri Sep 11 10:00:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7bv2_30210/09_2026/7bv2_30210.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bv2_30210/09_2026/7bv2_30210.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7bv2_30210/09_2026/7bv2_30210.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bv2_30210/09_2026/7bv2_30210.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7bv2_30210/09_2026/7bv2_30210.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bv2_30210/09_2026/7bv2_30210.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7bv2_30210/09_2026/7bv2_30210.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7bv2_30210/09_2026/7bv2_30210.cif" } resolution = 2.5 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= 0.014 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 Zn 2 6.06 5 P 28 5.49 5 Mg 2 5.21 5 S 58 5.16 5 C 5407 2.51 5 N 1437 2.21 5 O 1696 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8630 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 834, 6712 Classifications: {'peptide': 834} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 805} Chain breaks: 3 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASP:plan': 3} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 871 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 108} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 481 Classifications: {'peptide': 63} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 62} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "P" Number of atoms: 234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 234 Classifications: {'RNAv2': 11} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 5, 'rna3p_pyr': 5} Link IDs: {'rna2p': 1, 'rna3p': 9} Chain: "T" Number of atoms: 290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 290 Classifications: {'RNAv2': 14} Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 9} Link IDs: {'rna3p': 13} Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 13 Unusual residues: {' MG': 2, ' ZN': 2, 'POP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "P" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'F86': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1816 SG CYS A 301 49.560 64.092 38.924 1.00 12.33 S ATOM 1857 SG CYS A 306 49.369 63.471 35.242 1.00 10.05 S ATOM 1889 SG CYS A 310 52.744 63.249 37.074 1.00 9.56 S ATOM 3297 SG CYS A 487 31.730 59.229 47.521 1.00 11.38 S ATOM 4550 SG CYS A 645 30.654 59.341 44.075 1.00 12.29 S ATOM 4556 SG CYS A 646 33.652 60.861 45.159 1.00 10.15 S Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" O POP A1003 " occ=0.50 ... (7 atoms not shown) pdb=" P2 POP A1003 " occ=0.50 residue: pdb="MG MG A1004 " occ=0.50 residue: pdb="MG MG A1005 " occ=0.50 residue: pdb=" C1 F86 P 101 " occ=0.50 ... (22 atoms not shown) pdb=" P1 F86 P 101 " occ=0.50 Time building chain proxies: 1.97, per 1000 atoms: 0.23 Number of scatterers: 8630 At special positions: 0 Unit cell: (95.316, 93.288, 106.47, 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 S 58 16.00 P 28 15.00 Mg 2 11.99 O 1696 8.00 N 1437 7.00 C 5407 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.72 Conformation dependent library (CDL) restraints added in 227.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " Number of angles added : 6 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1936 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 8 sheets defined 56.4% alpha, 13.4% beta 9 base pairs and 19 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 84 through 90 Processing helix chain 'A' and resid 123 through 133 removed outlier: 3.534A pdb=" N LEU A 127 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 149 Processing helix chain 'A' and resid 153 through 159 removed outlier: 3.682A pdb=" N PHE A 157 " --> pdb=" O ASP A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 176 Processing helix chain 'A' and resid 178 through 200 Processing helix chain 'A' and resid 206 through 210 Processing helix chain 'A' and resid 234 through 248 Proline residue: A 243 - end of helix removed outlier: 4.045A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A 247 " --> pdb=" O PRO A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 260 removed outlier: 4.327A pdb=" N ALA A 253 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N VAL A 257 " --> pdb=" O GLU A 254 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ASP A 258 " --> pdb=" O SER A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 287 Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.522A pdb=" N PHE A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 326 Processing helix chain 'A' and resid 367 through 377 Processing helix chain 'A' and resid 377 through 385 removed outlier: 4.541A pdb=" N HIS A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 426 Processing helix chain 'A' and resid 447 through 454 Processing helix chain 'A' and resid 455 through 459 Processing helix chain 'A' and resid 465 through 477 removed outlier: 3.853A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 481 Processing helix chain 'A' and resid 489 through 493 removed outlier: 3.519A pdb=" N VAL A 493 " --> pdb=" O ALA A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 509 Processing helix chain 'A' and resid 511 through 519 removed outlier: 3.726A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 531 Processing helix chain 'A' and resid 561 through 582 removed outlier: 3.710A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 606 Processing helix chain 'A' and resid 621 through 626 removed outlier: 3.656A pdb=" N MET A 626 " --> pdb=" O CYS A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 639 Processing helix chain 'A' and resid 640 through 642 No H-bonds generated for 'chain 'A' and resid 640 through 642' Processing helix chain 'A' and resid 647 through 663 Processing helix chain 'A' and resid 686 through 709 Processing helix chain 'A' and resid 711 through 715 Processing helix chain 'A' and resid 717 through 733 Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 768 through 773 Processing helix chain 'A' and resid 778 through 790 Processing helix chain 'A' and resid 795 through 799 Processing helix chain 'A' and resid 833 through 842 Processing helix chain 'A' and resid 846 through 850 Processing helix chain 'A' and resid 851 through 867 removed outlier: 3.958A pdb=" N GLU A 857 " --> pdb=" O THR A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 872 Processing helix chain 'A' and resid 874 through 895 removed outlier: 4.207A pdb=" N VAL A 880 " --> pdb=" O GLU A 876 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N HIS A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 923 removed outlier: 4.306A pdb=" N TYR A 921 " --> pdb=" O GLU A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 926 No H-bonds generated for 'chain 'A' and resid 924 through 926' Processing helix chain 'B' and resid 79 through 94 Processing helix chain 'B' and resid 95 through 97 No H-bonds generated for 'chain 'B' and resid 95 through 97' Processing helix chain 'B' and resid 100 through 109 removed outlier: 4.036A pdb=" N ASN B 109 " --> pdb=" O ASN B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 125 removed outlier: 4.168A pdb=" N LEU B 122 " --> pdb=" O ASN B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 142 Processing helix chain 'B' and resid 168 through 172 Processing helix chain 'B' and resid 176 through 180 Processing helix chain 'C' and resid 3 through 20 Processing helix chain 'C' and resid 21 through 24 Processing helix chain 'C' and resid 25 through 42 removed outlier: 4.043A pdb=" N GLN C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 62 removed outlier: 3.827A pdb=" N VAL C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N MET C 62 " --> pdb=" O VAL C 58 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 38 Processing sheet with id=AA2, first strand: chain 'A' and resid 223 through 224 removed outlier: 7.094A pdb=" N ILE A 201 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N VAL A 233 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N GLY A 203 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 352 through 355 removed outlier: 6.653A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) removed outlier: 9.413A pdb=" N SER A 363 " --> pdb=" O LYS A 332 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N PHE A 334 " --> pdb=" O SER A 363 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 352 through 355 removed outlier: 6.653A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 556 through 559 removed outlier: 6.653A pdb=" N THR A 540 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LEU A 673 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N VAL A 398 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LEU A 388 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN B 158 " --> pdb=" O THR B 187 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 414 through 415 Processing sheet with id=AA7, first strand: chain 'A' and resid 753 through 758 Processing sheet with id=AA8, first strand: chain 'A' and resid 816 through 822 removed outlier: 3.688A pdb=" N ASP A 825 " --> pdb=" O GLN A 822 " (cutoff:3.500A) 420 hydrogen bonds defined for protein. 1107 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 20 hydrogen bonds 40 hydrogen bond angles 0 basepair planarities 9 basepair parallelities 19 stacking parallelities Total time for adding SS restraints: 1.40 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1344 1.29 - 1.43: 2552 1.43 - 1.56: 4834 1.56 - 1.70: 49 1.70 - 1.83: 88 Bond restraints: 8867 Sorted by residual: bond pdb=" O4 F86 P 101 " pdb=" P1 F86 P 101 " ideal model delta sigma weight residual 1.601 1.704 -0.103 1.00e-02 1.00e+04 1.06e+02 bond pdb=" C12 F86 P 101 " pdb=" N2 F86 P 101 " ideal model delta sigma weight residual 1.293 1.359 -0.066 1.00e-02 1.00e+04 4.38e+01 bond pdb=" C11 F86 P 101 " pdb=" N5 F86 P 101 " ideal model delta sigma weight residual 1.337 1.392 -0.055 1.00e-02 1.00e+04 3.07e+01 bond pdb=" P U P 20 " pdb=" O5' U P 20 " ideal model delta sigma weight residual 1.593 1.676 -0.083 2.00e-02 2.50e+03 1.73e+01 bond pdb=" O3' A P 19 " pdb=" P U P 20 " ideal model delta sigma weight residual 1.607 1.558 0.049 1.20e-02 6.94e+03 1.68e+01 ... (remaining 8862 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 11810 2.06 - 4.11: 296 4.11 - 6.17: 42 6.17 - 8.23: 4 8.23 - 10.28: 3 Bond angle restraints: 12155 Sorted by residual: angle pdb=" C10 F86 P 101 " pdb=" C9 F86 P 101 " pdb=" C11 F86 P 101 " ideal model delta sigma weight residual 136.68 128.29 8.39 1.00e+00 1.00e+00 7.04e+01 angle pdb=" C10 F86 P 101 " pdb=" C9 F86 P 101 " pdb=" N1 F86 P 101 " ideal model delta sigma weight residual 107.41 115.10 -7.69 1.00e+00 1.00e+00 5.91e+01 angle pdb=" C7 F86 P 101 " pdb=" C10 F86 P 101 " pdb=" C9 F86 P 101 " ideal model delta sigma weight residual 107.84 100.22 7.62 1.00e+00 1.00e+00 5.81e+01 angle pdb=" C3' A P 19 " pdb=" O3' A P 19 " pdb=" P U P 20 " ideal model delta sigma weight residual 119.70 125.93 -6.23 1.20e+00 6.94e-01 2.69e+01 angle pdb=" C5 F86 P 101 " pdb=" N1 F86 P 101 " pdb=" C9 F86 P 101 " ideal model delta sigma weight residual 109.66 105.27 4.39 1.00e+00 1.00e+00 1.93e+01 ... (remaining 12150 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.93: 4778 21.93 - 43.86: 367 43.86 - 65.79: 34 65.79 - 87.71: 11 87.71 - 109.64: 2 Dihedral angle restraints: 5192 sinusoidal: 2193 harmonic: 2999 Sorted by residual: dihedral pdb=" C4' G P 10 " pdb=" C3' G P 10 " pdb=" C2' G P 10 " pdb=" C1' G P 10 " ideal model delta sinusoidal sigma weight residual 36.34 -36.33 72.68 1 3.10e+00 1.04e-01 7.02e+02 dihedral pdb=" O4' G P 10 " pdb=" C4' G P 10 " pdb=" C3' G P 10 " pdb=" C2' G P 10 " ideal model delta sinusoidal sigma weight residual -35.15 26.01 -61.15 1 4.00e+00 6.25e-02 3.11e+02 dihedral pdb=" O4' G P 10 " pdb=" C2' G P 10 " pdb=" C1' G P 10 " pdb=" C3' G P 10 " ideal model delta sinusoidal sigma weight residual -94.41 -34.95 -59.46 3 3.80e+00 6.93e-02 1.48e+02 ... (remaining 5189 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1090 0.057 - 0.114: 226 0.114 - 0.171: 30 0.171 - 0.228: 27 0.228 - 0.285: 14 Chirality restraints: 1387 Sorted by residual: chirality pdb=" C2' G P 10 " pdb=" C3' G P 10 " pdb=" O2' G P 10 " pdb=" C1' G P 10 " both_signs ideal model delta sigma weight residual False -2.79 -2.50 -0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" P U P 20 " pdb=" OP1 U P 20 " pdb=" OP2 U P 20 " pdb=" O5' U P 20 " both_signs ideal model delta sigma weight residual True 2.17 -2.46 -0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" CA ARG B 111 " pdb=" N ARG B 111 " pdb=" C ARG B 111 " pdb=" CB ARG B 111 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 1384 not shown) Planarity restraints: 1452 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U P 20 " 0.066 2.00e-02 2.50e+03 3.19e-02 2.29e+01 pdb=" N1 U P 20 " -0.052 2.00e-02 2.50e+03 pdb=" C2 U P 20 " -0.025 2.00e-02 2.50e+03 pdb=" O2 U P 20 " 0.002 2.00e-02 2.50e+03 pdb=" N3 U P 20 " -0.006 2.00e-02 2.50e+03 pdb=" C4 U P 20 " 0.009 2.00e-02 2.50e+03 pdb=" O4 U P 20 " 0.030 2.00e-02 2.50e+03 pdb=" C5 U P 20 " -0.002 2.00e-02 2.50e+03 pdb=" C6 U P 20 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS C 36 " 0.017 2.00e-02 2.50e+03 1.80e-02 4.84e+00 pdb=" CG HIS C 36 " -0.039 2.00e-02 2.50e+03 pdb=" ND1 HIS C 36 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 HIS C 36 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 HIS C 36 " 0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS C 36 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 532 " 0.011 2.00e-02 2.50e+03 2.07e-02 4.27e+00 pdb=" C LYS A 532 " -0.036 2.00e-02 2.50e+03 pdb=" O LYS A 532 " 0.013 2.00e-02 2.50e+03 pdb=" N ARG A 533 " 0.012 2.00e-02 2.50e+03 ... (remaining 1449 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 31 2.53 - 3.12: 6388 3.12 - 3.72: 13413 3.72 - 4.31: 20117 4.31 - 4.90: 32232 Nonbonded interactions: 72181 Sorted by model distance: nonbonded pdb=" O4 U P 12 " pdb=" N1 A T 19 " model vdw 1.942 2.496 nonbonded pdb=" O ASN A 790 " pdb=" OD1 ASN A 790 " model vdw 2.135 3.040 nonbonded pdb=" O GLU A 144 " pdb=" OG1 THR A 148 " model vdw 2.248 3.040 nonbonded pdb=" O ILE A 494 " pdb=" NE2 GLN A 573 " model vdw 2.281 3.120 nonbonded pdb=" OG SER A 239 " pdb=" OD1 ASP A 465 " model vdw 2.284 3.040 ... (remaining 72176 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: 0.720 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 10.230 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:6.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 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 : 0.006 0.200 8876 Z= 0.344 Angle : 0.806 18.061 12161 Z= 0.455 Chirality : 0.059 0.285 1387 Planarity : 0.004 0.044 1452 Dihedral : 15.059 109.643 3256 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.03 (0.26), residues: 999 helix: -0.10 (0.23), residues: 472 sheet: -0.43 (0.47), residues: 97 loop : 0.56 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 914 TYR 0.024 0.002 TYR A 289 PHE 0.027 0.002 PHE A 652 TRP 0.015 0.002 TRP A 916 HIS 0.019 0.002 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.29 ( 8867) covalent geometry : angle 0.76513 / 0.45 (12155) hydrogen bonds : bond 0.17649 / 11.23 ( 429) hydrogen bonds : angle 6.48694 / 4.44 ( 1147) metal coordination : bond 0.07948 / 2.91 ( 8) metal coordination : angle 11.40962 / 6.07 ( 6) Misc. bond : bond 0.15822 / 8.33 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.330 Fit side-chains REVERT: A 160 LYS cc_start: 0.7734 (ttpp) cc_final: 0.7251 (ttpt) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.5300 time to fit residues: 86.2557 Evaluate side-chains 130 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 177 ASN A 191 GLN ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 790 ASN B 176 ASN ** C 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.160777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.117814 restraints weight = 8667.381| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 1.84 r_work: 0.3198 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3070 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 8 (14 function evaluations) r_final: 0.3070 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8876 Z= 0.162 Angle : 0.640 10.244 12161 Z= 0.326 Chirality : 0.051 0.693 1387 Planarity : 0.004 0.045 1452 Dihedral : 8.224 101.760 1402 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.36 % Allowed : 10.40 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.48 (0.26), residues: 999 helix: 0.46 (0.24), residues: 466 sheet: -0.06 (0.48), residues: 98 loop : 0.49 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 914 TYR 0.018 0.002 TYR A 289 PHE 0.023 0.002 PHE A 652 TRP 0.010 0.001 TRP A 916 HIS 0.014 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 ( 8867) covalent geometry : angle 0.63683 / 0.33 (12155) hydrogen bonds : bond 0.04818 / 3.13 ( 429) hydrogen bonds : angle 4.48133 / 3.05 ( 1147) metal coordination : bond 0.01345 / 0.65 ( 8) metal coordination : angle 2.75768 / 1.52 ( 6) Misc. bond : bond 0.00129 / 0.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 132 time to evaluate : 0.305 Fit side-chains REVERT: A 144 GLU cc_start: 0.8154 (tp30) cc_final: 0.7661 (tm-30) REVERT: A 158 ASN cc_start: 0.8162 (m-40) cc_final: 0.7839 (m-40) REVERT: A 796 GLU cc_start: 0.7099 (mm-30) cc_final: 0.6663 (mt-10) REVERT: C 62 MET cc_start: 0.6884 (ptp) cc_final: 0.6458 (ptp) outliers start: 12 outliers final: 3 residues processed: 134 average time/residue: 0.5582 time to fit residues: 79.8433 Evaluate side-chains 126 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 123 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 610 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 29 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 91 optimal weight: 0.5980 chunk 24 optimal weight: 0.0170 chunk 64 optimal weight: 7.9990 chunk 37 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 overall best weight: 1.0820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 177 ASN A 552 ASN A 724 GLN A 790 ASN B 176 ASN C 34 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.162729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.120313 restraints weight = 8637.656| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.82 r_work: 0.3233 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3106 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (12 function evaluations) r_final: 0.3106 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8876 Z= 0.119 Angle : 0.556 8.610 12161 Z= 0.281 Chirality : 0.046 0.390 1387 Planarity : 0.004 0.040 1452 Dihedral : 7.941 87.533 1402 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.03 % Allowed : 11.86 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 0.76 (0.26), residues: 999 helix: 0.84 (0.24), residues: 471 sheet: 0.22 (0.51), residues: 86 loop : 0.39 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 555 TYR 0.015 0.001 TYR A 788 PHE 0.019 0.001 PHE A 652 TRP 0.011 0.001 TRP A 916 HIS 0.012 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 ( 8867) covalent geometry : angle 0.55369 / 0.28 (12155) hydrogen bonds : bond 0.03858 / 2.51 ( 429) hydrogen bonds : angle 4.16309 / 2.80 ( 1147) metal coordination : bond 0.00843 / 0.48 ( 8) metal coordination : angle 2.24036 / 1.22 ( 6) Misc. bond : bond 0.00088 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 136 time to evaluate : 0.325 Fit side-chains REVERT: A 144 GLU cc_start: 0.8198 (tp30) cc_final: 0.7686 (tm-30) REVERT: A 158 ASN cc_start: 0.8056 (m-40) cc_final: 0.7855 (m-40) REVERT: A 796 GLU cc_start: 0.6953 (OUTLIER) cc_final: 0.6544 (mt-10) REVERT: B 174 MET cc_start: 0.7822 (tpp) cc_final: 0.7446 (tpt) REVERT: C 27 LYS cc_start: 0.7713 (ttpp) cc_final: 0.7513 (mtpp) REVERT: C 62 MET cc_start: 0.6706 (ptp) cc_final: 0.6436 (ptp) outliers start: 18 outliers final: 6 residues processed: 140 average time/residue: 0.5580 time to fit residues: 83.3057 Evaluate side-chains 128 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 121 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 796 GLU Chi-restraints excluded: chain B residue 169 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 31 optimal weight: 8.9990 chunk 1 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 43 optimal weight: 7.9990 chunk 84 optimal weight: 9.9990 chunk 56 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 381 HIS ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 724 GLN A 875 GLN B 158 GLN C 34 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.155173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.109511 restraints weight = 8791.085| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.82 r_work: 0.3115 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2989 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.2989 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.070 8876 Z= 0.410 Angle : 0.797 7.459 12161 Z= 0.410 Chirality : 0.059 0.249 1387 Planarity : 0.005 0.048 1452 Dihedral : 8.312 89.005 1402 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.26 % Allowed : 13.56 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.00 (0.26), residues: 999 helix: 0.28 (0.23), residues: 472 sheet: -0.24 (0.48), residues: 98 loop : -0.05 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 190 TYR 0.026 0.003 TYR A 149 PHE 0.029 0.003 PHE A 741 TRP 0.013 0.003 TRP A 290 HIS 0.009 0.002 HIS A 642 Details of bonding type rmsd/Z covalent geometry : bond 0.00988 / 0.41 ( 8867) covalent geometry : angle 0.79295 / 0.41 (12155) hydrogen bonds : bond 0.06640 / 4.33 ( 429) hydrogen bonds : angle 4.69797 / 3.24 ( 1147) metal coordination : bond 0.02827 / 1.34 ( 8) metal coordination : angle 3.89631 / 2.04 ( 6) Misc. bond : bond 0.00293 / 0.15 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 0.316 Fit side-chains REVERT: A 149 TYR cc_start: 0.8561 (m-80) cc_final: 0.8279 (m-80) REVERT: A 284 ASP cc_start: 0.8276 (OUTLIER) cc_final: 0.8074 (m-30) REVERT: A 796 GLU cc_start: 0.7034 (mm-30) cc_final: 0.6617 (mt-10) REVERT: A 885 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7293 (mp) REVERT: B 174 MET cc_start: 0.7791 (tpp) cc_final: 0.7459 (tpt) REVERT: C 23 GLU cc_start: 0.8033 (pt0) cc_final: 0.7734 (pt0) REVERT: C 62 MET cc_start: 0.6895 (ptp) cc_final: 0.6564 (ptp) outliers start: 20 outliers final: 7 residues processed: 134 average time/residue: 0.5830 time to fit residues: 83.2515 Evaluate side-chains 125 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 116 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain C residue 22 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 38 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 158 ASN A 177 ASN ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** 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 = 0.3880 r_free = 0.3880 target = 0.162306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.117409 restraints weight = 8738.255| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.81 r_work: 0.3217 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3088 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3088 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8876 Z= 0.108 Angle : 0.541 8.273 12161 Z= 0.272 Chirality : 0.044 0.354 1387 Planarity : 0.004 0.043 1452 Dihedral : 7.940 82.905 1402 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.02 % Allowed : 14.92 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 0.59 (0.26), residues: 999 helix: 0.86 (0.24), residues: 471 sheet: -0.05 (0.47), residues: 96 loop : 0.14 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 555 TYR 0.020 0.001 TYR B 135 PHE 0.018 0.001 PHE A 652 TRP 0.011 0.001 TRP A 916 HIS 0.010 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 ( 8867) covalent geometry : angle 0.53853 / 0.27 (12155) hydrogen bonds : bond 0.03582 / 2.33 ( 429) hydrogen bonds : angle 4.12290 / 2.77 ( 1147) metal coordination : bond 0.00641 / 0.37 ( 8) metal coordination : angle 2.24894 / 1.22 ( 6) Misc. bond : bond 0.00096 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 127 time to evaluate : 0.322 Fit side-chains REVERT: A 158 ASN cc_start: 0.8089 (m110) cc_final: 0.7838 (m-40) REVERT: A 284 ASP cc_start: 0.8215 (OUTLIER) cc_final: 0.7975 (t70) REVERT: A 542 MET cc_start: 0.8070 (OUTLIER) cc_final: 0.7815 (mmm) REVERT: A 796 GLU cc_start: 0.6908 (mm-30) cc_final: 0.6505 (mt-10) REVERT: A 885 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7113 (mp) REVERT: B 174 MET cc_start: 0.7835 (tpp) cc_final: 0.7536 (tpt) REVERT: C 27 LYS cc_start: 0.7774 (ttpp) cc_final: 0.7564 (mtpp) REVERT: C 62 MET cc_start: 0.6679 (ptp) cc_final: 0.6433 (ptp) outliers start: 9 outliers final: 3 residues processed: 130 average time/residue: 0.5881 time to fit residues: 81.3280 Evaluate side-chains 126 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 120 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 885 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 53 optimal weight: 6.9990 chunk 67 optimal weight: 7.9990 chunk 62 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 1 optimal weight: 8.9990 chunk 22 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 177 ASN A 468 GLN ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** 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 = 0.3842 r_free = 0.3842 target = 0.158709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.113322 restraints weight = 8680.007| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.80 r_work: 0.3162 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3032 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.3032 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8876 Z= 0.196 Angle : 0.603 7.470 12161 Z= 0.308 Chirality : 0.047 0.230 1387 Planarity : 0.004 0.044 1452 Dihedral : 7.966 79.350 1402 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.47 % Allowed : 15.59 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 0.45 (0.26), residues: 999 helix: 0.76 (0.24), residues: 471 sheet: -0.32 (0.52), residues: 76 loop : 0.07 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 555 TYR 0.019 0.002 TYR A 788 PHE 0.022 0.002 PHE A 652 TRP 0.011 0.002 TRP A 916 HIS 0.008 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.20 ( 8867) covalent geometry : angle 0.59999 / 0.31 (12155) hydrogen bonds : bond 0.04763 / 3.11 ( 429) hydrogen bonds : angle 4.27775 / 2.92 ( 1147) metal coordination : bond 0.01612 / 0.77 ( 8) metal coordination : angle 2.56392 / 1.39 ( 6) Misc. bond : bond 0.00159 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 0.338 Fit side-chains REVERT: A 158 ASN cc_start: 0.8093 (m110) cc_final: 0.7878 (m-40) REVERT: A 284 ASP cc_start: 0.8211 (OUTLIER) cc_final: 0.7984 (t70) REVERT: A 542 MET cc_start: 0.8301 (OUTLIER) cc_final: 0.7958 (mmm) REVERT: A 796 GLU cc_start: 0.7017 (mm-30) cc_final: 0.6613 (mt-10) REVERT: B 174 MET cc_start: 0.7746 (tpp) cc_final: 0.7447 (tpt) REVERT: C 62 MET cc_start: 0.6755 (ptp) cc_final: 0.6489 (ptp) outliers start: 13 outliers final: 5 residues processed: 126 average time/residue: 0.6074 time to fit residues: 81.2197 Evaluate side-chains 123 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 116 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 610 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 85 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 78 optimal weight: 6.9990 chunk 44 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 886 GLN C 34 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.161115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.116351 restraints weight = 8734.299| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.79 r_work: 0.3204 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3072 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3072 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8876 Z= 0.124 Angle : 0.544 7.560 12161 Z= 0.275 Chirality : 0.044 0.262 1387 Planarity : 0.004 0.042 1452 Dihedral : 7.866 77.716 1402 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.47 % Allowed : 16.16 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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 (0.26), residues: 999 helix: 0.95 (0.24), residues: 471 sheet: 0.06 (0.49), residues: 96 loop : 0.12 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 555 TYR 0.022 0.001 TYR B 135 PHE 0.018 0.001 PHE A 652 TRP 0.010 0.001 TRP A 916 HIS 0.008 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 ( 8867) covalent geometry : angle 0.54186 / 0.27 (12155) hydrogen bonds : bond 0.03780 / 2.46 ( 429) hydrogen bonds : angle 4.10617 / 2.77 ( 1147) metal coordination : bond 0.00927 / 0.49 ( 8) metal coordination : angle 2.16928 / 1.18 ( 6) Misc. bond : bond 0.00108 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 122 time to evaluate : 0.321 Fit side-chains REVERT: A 136 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.6905 (pp20) REVERT: A 158 ASN cc_start: 0.8040 (m110) cc_final: 0.7829 (m-40) REVERT: A 284 ASP cc_start: 0.8194 (OUTLIER) cc_final: 0.7955 (t70) REVERT: A 542 MET cc_start: 0.8159 (OUTLIER) cc_final: 0.7830 (mmm) REVERT: A 610 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7289 (mt-10) REVERT: A 796 GLU cc_start: 0.6991 (OUTLIER) cc_final: 0.6582 (mt-10) REVERT: A 885 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.6992 (mp) REVERT: B 174 MET cc_start: 0.7820 (tpp) cc_final: 0.7545 (tpt) REVERT: C 23 GLU cc_start: 0.7698 (pt0) cc_final: 0.7394 (tt0) REVERT: C 27 LYS cc_start: 0.7795 (ttpp) cc_final: 0.7568 (mtpp) REVERT: C 62 MET cc_start: 0.6701 (ptp) cc_final: 0.6425 (ptp) outliers start: 13 outliers final: 4 residues processed: 128 average time/residue: 0.6499 time to fit residues: 88.3141 Evaluate side-chains 126 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 796 GLU Chi-restraints excluded: chain A residue 885 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 58 optimal weight: 8.9990 chunk 51 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 886 GLN C 34 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.158059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.112988 restraints weight = 8679.385| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.79 r_work: 0.3160 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3028 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3028 r_free = 0.3028 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3028 r_free = 0.3028 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.3028 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8876 Z= 0.208 Angle : 0.610 7.303 12161 Z= 0.312 Chirality : 0.047 0.213 1387 Planarity : 0.004 0.044 1452 Dihedral : 7.934 79.035 1402 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.03 % Allowed : 16.05 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 0.48 (0.26), residues: 999 helix: 0.78 (0.24), residues: 472 sheet: -0.03 (0.50), residues: 94 loop : 0.05 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 889 TYR 0.020 0.002 TYR A 788 PHE 0.022 0.002 PHE A 741 TRP 0.011 0.002 TRP A 916 HIS 0.007 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.21 ( 8867) covalent geometry : angle 0.60769 / 0.31 (12155) hydrogen bonds : bond 0.04867 / 3.17 ( 429) hydrogen bonds : angle 4.29744 / 2.94 ( 1147) metal coordination : bond 0.01684 / 0.81 ( 8) metal coordination : angle 2.68439 / 1.44 ( 6) Misc. bond : bond 0.00166 / 0.09 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 0.318 Fit side-chains REVERT: A 158 ASN cc_start: 0.8078 (m110) cc_final: 0.7850 (m-40) REVERT: A 284 ASP cc_start: 0.8229 (OUTLIER) cc_final: 0.7976 (t70) REVERT: A 542 MET cc_start: 0.8322 (OUTLIER) cc_final: 0.7980 (mmm) REVERT: A 610 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7575 (mt-10) REVERT: A 796 GLU cc_start: 0.7022 (OUTLIER) cc_final: 0.6624 (mt-10) REVERT: A 914 ARG cc_start: 0.6628 (mtp85) cc_final: 0.6139 (mmm-85) REVERT: B 174 MET cc_start: 0.7786 (tpp) cc_final: 0.7481 (tpt) REVERT: C 23 GLU cc_start: 0.7833 (pt0) cc_final: 0.7374 (tt0) REVERT: C 27 LYS cc_start: 0.7755 (ttpp) cc_final: 0.7487 (mtpp) REVERT: C 62 MET cc_start: 0.6846 (ptp) cc_final: 0.6614 (ptp) outliers start: 18 outliers final: 8 residues processed: 132 average time/residue: 0.6261 time to fit residues: 87.8854 Evaluate side-chains 131 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 730 CYS Chi-restraints excluded: chain A residue 796 GLU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 155 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 28 optimal weight: 7.9990 chunk 101 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 chunk 91 optimal weight: 0.4980 chunk 36 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 177 ASN ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 886 GLN C 34 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** 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 = 0.3886 r_free = 0.3886 target = 0.162913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.118109 restraints weight = 8655.959| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 1.80 r_work: 0.3225 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3097 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3097 r_free = 0.3097 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3097 r_free = 0.3097 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3097 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 8876 Z= 0.101 Angle : 0.521 7.453 12161 Z= 0.261 Chirality : 0.042 0.246 1387 Planarity : 0.004 0.042 1452 Dihedral : 7.805 77.196 1402 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.24 % Allowed : 17.18 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 0.79 (0.26), residues: 999 helix: 1.06 (0.24), residues: 471 sheet: 0.30 (0.53), residues: 86 loop : 0.13 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 555 TYR 0.014 0.001 TYR A 788 PHE 0.016 0.001 PHE A 652 TRP 0.008 0.001 TRP A 916 HIS 0.009 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 ( 8867) covalent geometry : angle 0.51867 / 0.26 (12155) hydrogen bonds : bond 0.03365 / 2.19 ( 429) hydrogen bonds : angle 4.03735 / 2.71 ( 1147) metal coordination : bond 0.00745 / 0.42 ( 8) metal coordination : angle 2.13458 / 1.16 ( 6) Misc. bond : bond 0.00086 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 124 time to evaluate : 0.312 Fit side-chains REVERT: A 158 ASN cc_start: 0.8067 (m110) cc_final: 0.7861 (m-40) REVERT: A 284 ASP cc_start: 0.8178 (OUTLIER) cc_final: 0.7951 (t70) REVERT: A 513 ARG cc_start: 0.7802 (ttm-80) cc_final: 0.7549 (ttm-80) REVERT: A 542 MET cc_start: 0.8093 (OUTLIER) cc_final: 0.7832 (mmm) REVERT: A 610 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7300 (mt-10) REVERT: A 796 GLU cc_start: 0.6970 (OUTLIER) cc_final: 0.6555 (mt-10) REVERT: A 922 GLU cc_start: 0.7822 (tt0) cc_final: 0.7496 (tt0) REVERT: C 23 GLU cc_start: 0.7684 (pt0) cc_final: 0.7379 (tt0) REVERT: C 27 LYS cc_start: 0.7659 (ttpp) cc_final: 0.7412 (mtpp) REVERT: C 62 MET cc_start: 0.6565 (ptp) cc_final: 0.6292 (ptp) outliers start: 11 outliers final: 4 residues processed: 129 average time/residue: 0.6247 time to fit residues: 85.7094 Evaluate side-chains 125 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 117 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 796 GLU Chi-restraints excluded: chain A residue 912 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 77 optimal weight: 5.9990 chunk 71 optimal weight: 0.2980 chunk 43 optimal weight: 10.0000 chunk 96 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 27 optimal weight: 8.9990 chunk 45 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 177 ASN ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 886 GLN C 34 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** 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 = 0.3845 r_free = 0.3845 target = 0.158832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.113828 restraints weight = 8622.060| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.78 r_work: 0.3169 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3040 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3040 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8876 Z= 0.184 Angle : 0.594 7.573 12161 Z= 0.301 Chirality : 0.046 0.208 1387 Planarity : 0.004 0.042 1452 Dihedral : 7.873 78.532 1402 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.13 % Allowed : 17.51 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 0.61 (0.26), residues: 999 helix: 0.89 (0.24), residues: 471 sheet: 0.38 (0.54), residues: 82 loop : 0.03 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 555 TYR 0.019 0.002 TYR A 788 PHE 0.021 0.002 PHE A 741 TRP 0.012 0.002 TRP A 916 HIS 0.007 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.18 ( 8867) covalent geometry : angle 0.59142 / 0.30 (12155) hydrogen bonds : bond 0.04566 / 2.98 ( 429) hydrogen bonds : angle 4.20666 / 2.87 ( 1147) metal coordination : bond 0.01491 / 0.73 ( 8) metal coordination : angle 2.48712 / 1.35 ( 6) Misc. bond : bond 0.00146 / 0.08 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 120 time to evaluate : 0.343 Fit side-chains REVERT: A 158 ASN cc_start: 0.8111 (m110) cc_final: 0.7877 (m-40) REVERT: A 284 ASP cc_start: 0.8239 (OUTLIER) cc_final: 0.8009 (t70) REVERT: A 542 MET cc_start: 0.8299 (OUTLIER) cc_final: 0.7955 (mmm) REVERT: A 610 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7520 (mt-10) REVERT: A 796 GLU cc_start: 0.7021 (OUTLIER) cc_final: 0.6622 (mt-10) REVERT: A 914 ARG cc_start: 0.6449 (mtp85) cc_final: 0.5983 (mmm-85) REVERT: C 23 GLU cc_start: 0.7810 (pt0) cc_final: 0.7370 (tt0) REVERT: C 27 LYS cc_start: 0.7731 (ttpp) cc_final: 0.7465 (mtpp) REVERT: C 62 MET cc_start: 0.6593 (ptp) cc_final: 0.6332 (ptp) outliers start: 10 outliers final: 5 residues processed: 124 average time/residue: 0.6149 time to fit residues: 80.8866 Evaluate side-chains 128 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 119 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 796 GLU Chi-restraints excluded: chain A residue 912 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 7 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 79 optimal weight: 0.0030 chunk 59 optimal weight: 0.6980 chunk 100 optimal weight: 7.9990 chunk 73 optimal weight: 4.9990 overall best weight: 1.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 886 GLN C 34 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.166301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.123054 restraints weight = 9041.856| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 1.88 r_work: 0.3450 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3327 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3327 r_free = 0.3327 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3327 r_free = 0.3327 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (12 function evaluations) r_final: 0.3327 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8876 Z= 0.133 Angle : 0.553 7.351 12161 Z= 0.280 Chirality : 0.044 0.207 1387 Planarity : 0.004 0.042 1452 Dihedral : 7.818 77.666 1402 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.24 % Allowed : 17.63 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.26), residues: 999 helix: 0.99 (0.24), residues: 471 sheet: 0.28 (0.51), residues: 92 loop : 0.08 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 555 TYR 0.016 0.001 TYR A 788 PHE 0.018 0.001 PHE A 741 TRP 0.007 0.001 TRP A 916 HIS 0.008 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 ( 8867) covalent geometry : angle 0.55072 / 0.28 (12155) hydrogen bonds : bond 0.03861 / 2.52 ( 429) hydrogen bonds : angle 4.10486 / 2.78 ( 1147) metal coordination : bond 0.01045 / 0.55 ( 8) metal coordination : angle 2.22521 / 1.21 ( 6) Misc. bond : bond 0.00109 / 0.06 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3657.00 seconds wall clock time: 62 minutes 52.60 seconds (3772.60 seconds total)