Starting phenix.real_space_refine on Tue Mar 3 22:02:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bv2_30210/03_2026/7bv2_30210.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bv2_30210/03_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_30210/03_2026/7bv2_30210.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bv2_30210/03_2026/7bv2_30210.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7bv2_30210/03_2026/7bv2_30210.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bv2_30210/03_2026/7bv2_30210.map" } 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-dev-5986/lib/python3.9/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: {'RNA': 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: {'RNA': 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: 1.91, per 1000 atoms: 0.22 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: 0.82 Conformation dependent library (CDL) restraints added in 326.3 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: 0.97 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: 1.32 Time building geometry restraints manager: 1.00 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=" P U P 20 " pdb=" O5' U P 20 " ideal model delta sigma weight residual 1.593 1.676 -0.083 1.50e-02 4.44e+03 3.08e+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=" O5 F86 P 101 " pdb=" P1 F86 P 101 " ideal model delta sigma weight residual 1.533 1.483 0.050 1.50e-02 4.44e+03 1.11e+01 ... (remaining 8862 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.75: 12102 3.75 - 7.50: 47 7.50 - 11.25: 5 11.25 - 15.00: 0 15.00 - 18.75: 1 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=" P1 POP A1003 " pdb=" O POP A1003 " pdb=" P2 POP A1003 " ideal model delta sigma weight residual 139.66 120.91 18.75 3.00e+00 1.11e-01 3.91e+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 - 17.97: 4697 17.97 - 35.93: 426 35.93 - 53.90: 99 53.90 - 71.87: 33 71.87 - 89.84: 9 Dihedral angle restraints: 5264 sinusoidal: 2265 harmonic: 2999 Sorted by residual: dihedral pdb=" CA TYR A 606 " pdb=" C TYR A 606 " pdb=" N SER A 607 " pdb=" CA SER A 607 " ideal model delta harmonic sigma weight residual -180.00 -148.17 -31.83 0 5.00e+00 4.00e-02 4.05e+01 dihedral pdb=" CA PRO A 612 " pdb=" C PRO A 612 " pdb=" N HIS A 613 " pdb=" CA HIS A 613 " ideal model delta harmonic sigma weight residual 180.00 157.13 22.87 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" CA ASN A 611 " pdb=" C ASN A 611 " pdb=" N PRO A 612 " pdb=" CA PRO A 612 " ideal model delta harmonic sigma weight residual -180.00 -157.80 -22.20 0 5.00e+00 4.00e-02 1.97e+01 ... (remaining 5261 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1063 0.052 - 0.103: 258 0.103 - 0.155: 52 0.155 - 0.207: 8 0.207 - 0.258: 6 Chirality restraints: 1387 Sorted by residual: 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 chirality pdb=" CA ASP A 258 " pdb=" N ASP A 258 " pdb=" C ASP A 258 " pdb=" CB ASP A 258 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CA LYS A 676 " pdb=" N LYS A 676 " pdb=" C LYS A 676 " pdb=" CB LYS A 676 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.35e+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: 0.400 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: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 10.350 Find NCS groups from input model: 0.030 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:6.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 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= 0.350 Angle : 0.785 18.748 12161 Z= 0.454 Chirality : 0.050 0.258 1387 Planarity : 0.004 0.044 1452 Dihedral : 15.369 89.836 3328 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 covalent geometry : bond 0.00491 ( 8867) covalent geometry : angle 0.74356 (12155) hydrogen bonds : bond 0.17649 ( 429) hydrogen bonds : angle 6.48694 ( 1147) metal coordination : bond 0.07948 ( 8) metal coordination : angle 11.40962 ( 6) Misc. bond : bond 0.15822 ( 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 : 0.303 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: 0.5326 time to fit residues: 86.3371 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 : 0.233 ------------------------------------------------------------------------------- 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: 8.9990 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3870 r_free = 0.3870 target = 0.160873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.117534 restraints weight = 8636.161| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.83 r_work: 0.3201 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3074 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3073 r_free = 0.3073 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3073 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1323 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= 0.159 Angle : 0.571 7.624 12161 Z= 0.311 Chirality : 0.043 0.179 1387 Planarity : 0.004 0.045 1452 Dihedral : 10.620 73.145 1474 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.24 % Allowed : 10.62 % Favored : 88.14 % 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: -0.05 (0.48), residues: 98 loop : 0.49 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 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 covalent geometry : bond 0.00366 ( 8867) covalent geometry : angle 0.56758 (12155) hydrogen bonds : bond 0.04833 ( 429) hydrogen bonds : angle 4.47950 ( 1147) metal coordination : bond 0.01311 ( 8) metal coordination : angle 2.72478 ( 6) Misc. bond : bond 0.00082 ( 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: 11 poor density : 133 time to evaluate : 0.273 Fit side-chains REVERT: A 144 GLU cc_start: 0.8148 (tp30) cc_final: 0.7655 (tm-30) REVERT: A 158 ASN cc_start: 0.8161 (m-40) cc_final: 0.7834 (m-40) REVERT: A 796 GLU cc_start: 0.7097 (mm-30) cc_final: 0.6669 (mt-10) REVERT: C 62 MET cc_start: 0.6887 (ptp) cc_final: 0.6461 (ptp) outliers start: 11 outliers final: 3 residues processed: 135 average time/residue: 0.5651 time to fit residues: 81.3223 Evaluate side-chains 128 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 125 time to evaluate : 0.231 ------------------------------------------------------------------------------- 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: 0.0770 chunk 15 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 59 optimal weight: 0.0270 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 705 ASN A 724 GLN A 790 ASN B 176 ASN 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 = 0.3913 r_free = 0.3913 target = 0.164877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.121582 restraints weight = 8598.820| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.97 r_work: 0.3267 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3138 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3138 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8876 Z= 0.096 Angle : 0.470 6.717 12161 Z= 0.253 Chirality : 0.039 0.191 1387 Planarity : 0.004 0.039 1452 Dihedral : 10.355 73.417 1474 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.81 % Allowed : 11.53 % Favored : 86.67 % 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: 0.86 (0.26), residues: 999 helix: 0.92 (0.24), residues: 471 sheet: 0.33 (0.52), residues: 84 loop : 0.43 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 555 TYR 0.013 0.001 TYR A 289 PHE 0.016 0.001 PHE A 652 TRP 0.011 0.001 TRP A 916 HIS 0.011 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00201 ( 8867) covalent geometry : angle 0.46739 (12155) hydrogen bonds : bond 0.03397 ( 429) hydrogen bonds : angle 4.09677 ( 1147) metal coordination : bond 0.00607 ( 8) metal coordination : angle 2.07265 ( 6) Misc. bond : bond 0.00062 ( 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 160 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 144 time to evaluate : 0.331 Fit side-chains REVERT: A 144 GLU cc_start: 0.8185 (tp30) cc_final: 0.7680 (tm-30) REVERT: A 796 GLU cc_start: 0.6956 (OUTLIER) cc_final: 0.6542 (mt-10) REVERT: B 174 MET cc_start: 0.7843 (tpp) cc_final: 0.7549 (tpt) REVERT: C 62 MET cc_start: 0.6690 (ptp) cc_final: 0.6391 (ptp) outliers start: 16 outliers final: 5 residues processed: 146 average time/residue: 0.5667 time to fit residues: 87.9068 Evaluate side-chains 135 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 129 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 1 optimal weight: 5.9990 chunk 63 optimal weight: 8.9990 chunk 6 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 chunk 43 optimal weight: 6.9990 chunk 84 optimal weight: 8.9990 chunk 56 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN A 177 ASN A 381 HIS A 552 ASN A 695 ASN A 705 ASN C 34 GLN C 36 HIS C 37 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.155279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.109511 restraints weight = 8769.151| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.82 r_work: 0.3118 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2988 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2988 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.071 8876 Z= 0.417 Angle : 0.750 7.102 12161 Z= 0.405 Chirality : 0.055 0.203 1387 Planarity : 0.006 0.048 1452 Dihedral : 10.996 73.101 1474 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.71 % Allowed : 13.45 % Favored : 83.84 % 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: 0.04 (0.26), residues: 999 helix: 0.30 (0.23), residues: 470 sheet: -0.16 (0.49), residues: 96 loop : -0.04 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 654 TYR 0.027 0.003 TYR A 149 PHE 0.030 0.004 PHE A 741 TRP 0.014 0.003 TRP A 290 HIS 0.009 0.002 HIS A 642 Details of bonding type rmsd covalent geometry : bond 0.01006 ( 8867) covalent geometry : angle 0.74520 (12155) hydrogen bonds : bond 0.06670 ( 429) hydrogen bonds : angle 4.68139 ( 1147) metal coordination : bond 0.02763 ( 8) metal coordination : angle 3.84190 ( 6) Misc. bond : bond 0.00302 ( 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 141 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 0.295 Fit side-chains REVERT: A 136 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.6647 (pp20) REVERT: A 149 TYR cc_start: 0.8548 (m-80) cc_final: 0.8268 (m-80) REVERT: A 158 ASN cc_start: 0.8199 (m110) cc_final: 0.7935 (m-40) REVERT: A 284 ASP cc_start: 0.8271 (OUTLIER) cc_final: 0.8069 (m-30) REVERT: A 417 LYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7768 (tttm) REVERT: A 452 ASP cc_start: 0.8448 (t0) cc_final: 0.8216 (t0) REVERT: A 796 GLU cc_start: 0.7087 (mm-30) cc_final: 0.6669 (mt-10) REVERT: A 885 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7229 (mp) REVERT: B 174 MET cc_start: 0.7885 (tpp) cc_final: 0.7541 (tpt) REVERT: C 62 MET cc_start: 0.6871 (ptp) cc_final: 0.6522 (ptp) outliers start: 24 outliers final: 8 residues processed: 132 average time/residue: 0.5886 time to fit residues: 82.3936 Evaluate side-chains 126 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 GLU 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 416 ASN Chi-restraints excluded: chain A residue 417 LYS 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 Chi-restraints excluded: chain C residue 55 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 38 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 99 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 34 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.161411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.116027 restraints weight = 8653.776| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.81 r_work: 0.3201 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3075 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3075 r_free = 0.3075 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3075 r_free = 0.3075 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3075 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8876 Z= 0.113 Angle : 0.490 7.090 12161 Z= 0.265 Chirality : 0.040 0.191 1387 Planarity : 0.004 0.043 1452 Dihedral : 10.596 73.225 1474 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.69 % Allowed : 14.58 % Favored : 83.73 % 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: 0.54 (0.26), residues: 999 helix: 0.80 (0.24), residues: 471 sheet: 0.06 (0.50), residues: 86 loop : 0.10 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 555 TYR 0.018 0.001 TYR A 289 PHE 0.018 0.001 PHE A 652 TRP 0.009 0.001 TRP A 916 HIS 0.003 0.001 HIS A 872 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 8867) covalent geometry : angle 0.48751 (12155) hydrogen bonds : bond 0.03763 ( 429) hydrogen bonds : angle 4.15047 ( 1147) metal coordination : bond 0.00722 ( 8) metal coordination : angle 2.31577 ( 6) Misc. bond : bond 0.00101 ( 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 139 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 0.329 Fit side-chains REVERT: A 136 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.6776 (pp20) REVERT: A 158 ASN cc_start: 0.8032 (m110) cc_final: 0.7798 (m-40) REVERT: A 284 ASP cc_start: 0.8226 (OUTLIER) cc_final: 0.7982 (t70) REVERT: A 417 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7930 (tttm) REVERT: A 796 GLU cc_start: 0.6913 (mm-30) cc_final: 0.6518 (mt-10) REVERT: A 885 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7096 (mp) REVERT: B 174 MET cc_start: 0.7829 (tpp) cc_final: 0.7516 (tpt) REVERT: C 62 MET cc_start: 0.6718 (ptp) cc_final: 0.6449 (ptp) outliers start: 15 outliers final: 5 residues processed: 130 average time/residue: 0.6098 time to fit residues: 83.9151 Evaluate side-chains 127 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 118 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 GLU 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 416 ASN Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain A residue 450 ILE 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: 6.9990 chunk 62 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 71 optimal weight: 0.5980 chunk 31 optimal weight: 7.9990 chunk 77 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 22 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 552 ASN C 34 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.160621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.117186 restraints weight = 8627.479| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.94 r_work: 0.3196 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3065 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3065 r_free = 0.3065 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3065 r_free = 0.3065 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3065 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8876 Z= 0.135 Angle : 0.499 6.785 12161 Z= 0.269 Chirality : 0.040 0.154 1387 Planarity : 0.004 0.042 1452 Dihedral : 10.578 73.325 1474 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.03 % Allowed : 15.48 % Favored : 82.49 % 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: 0.87 (0.24), residues: 471 sheet: 0.13 (0.51), residues: 86 loop : 0.11 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 555 TYR 0.018 0.002 TYR A 289 PHE 0.019 0.001 PHE A 652 TRP 0.010 0.001 TRP A 916 HIS 0.003 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 8867) covalent geometry : angle 0.49655 (12155) hydrogen bonds : bond 0.04026 ( 429) hydrogen bonds : angle 4.14225 ( 1147) metal coordination : bond 0.01141 ( 8) metal coordination : angle 2.19418 ( 6) Misc. bond : bond 0.00127 ( 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 142 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 0.286 Fit side-chains REVERT: A 136 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.6907 (pp20) REVERT: A 158 ASN cc_start: 0.8126 (m110) cc_final: 0.7901 (m-40) REVERT: A 284 ASP cc_start: 0.8267 (OUTLIER) cc_final: 0.8039 (t70) REVERT: A 417 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.7981 (tttm) REVERT: A 542 MET cc_start: 0.8262 (OUTLIER) cc_final: 0.7912 (mmm) REVERT: A 610 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7349 (mt-10) REVERT: A 796 GLU cc_start: 0.7019 (OUTLIER) cc_final: 0.6612 (mt-10) REVERT: A 885 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7165 (mp) REVERT: B 174 MET cc_start: 0.7850 (tpp) cc_final: 0.7542 (tpt) REVERT: C 62 MET cc_start: 0.6682 (ptp) cc_final: 0.6478 (ptp) outliers start: 18 outliers final: 5 residues processed: 132 average time/residue: 0.6227 time to fit residues: 87.0190 Evaluate side-chains 129 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 117 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 GLU 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 416 ASN Chi-restraints excluded: chain A residue 417 LYS 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 731 LEU Chi-restraints excluded: chain A residue 796 GLU Chi-restraints excluded: chain A residue 885 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 85 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 chunk 61 optimal weight: 0.9980 chunk 78 optimal weight: 7.9990 chunk 44 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 468 GLN A 552 ASN A 886 GLN C 34 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.159205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.113855 restraints weight = 8709.820| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.81 r_work: 0.3171 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- 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 = 0.40 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 = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3040 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8876 Z= 0.177 Angle : 0.538 7.063 12161 Z= 0.291 Chirality : 0.042 0.145 1387 Planarity : 0.004 0.043 1452 Dihedral : 10.669 73.275 1474 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.37 % Allowed : 15.37 % Favored : 82.26 % 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: 0.56 (0.26), residues: 999 helix: 0.82 (0.24), residues: 471 sheet: 0.16 (0.52), residues: 86 loop : 0.08 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 555 TYR 0.019 0.002 TYR B 135 PHE 0.021 0.002 PHE A 741 TRP 0.011 0.002 TRP A 916 HIS 0.003 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 8867) covalent geometry : angle 0.53550 (12155) hydrogen bonds : bond 0.04518 ( 429) hydrogen bonds : angle 4.22918 ( 1147) metal coordination : bond 0.01453 ( 8) metal coordination : angle 2.50927 ( 6) Misc. bond : bond 0.00146 ( 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 139 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 0.296 Fit side-chains REVERT: A 136 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.6850 (pp20) REVERT: A 158 ASN cc_start: 0.8108 (m110) cc_final: 0.7871 (m-40) REVERT: A 284 ASP cc_start: 0.8229 (OUTLIER) cc_final: 0.7990 (t70) REVERT: A 370 GLU cc_start: 0.7142 (mt-10) cc_final: 0.6928 (mt-10) REVERT: A 417 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7887 (tttm) REVERT: A 542 MET cc_start: 0.8297 (OUTLIER) cc_final: 0.7946 (mmm) REVERT: A 610 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7453 (mt-10) REVERT: A 796 GLU cc_start: 0.7012 (OUTLIER) cc_final: 0.6608 (mt-10) REVERT: A 885 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7129 (mp) REVERT: B 174 MET cc_start: 0.7774 (tpp) cc_final: 0.7472 (tpt) REVERT: C 23 GLU cc_start: 0.7776 (pt0) cc_final: 0.7404 (tt0) REVERT: C 62 MET cc_start: 0.6739 (ptp) cc_final: 0.6469 (ptp) outliers start: 21 outliers final: 9 residues processed: 129 average time/residue: 0.6513 time to fit residues: 88.9295 Evaluate side-chains 134 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 136 GLU 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 416 ASN Chi-restraints excluded: chain A residue 417 LYS 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 885 LEU Chi-restraints excluded: chain C residue 22 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 58 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 11 optimal weight: 6.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 ASN ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 886 GLN C 34 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.162858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.117946 restraints weight = 8695.291| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.80 r_work: 0.3226 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3096 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3096 r_free = 0.3096 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 = 0.3096 r_free = 0.3096 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3096 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8876 Z= 0.103 Angle : 0.467 6.683 12161 Z= 0.250 Chirality : 0.039 0.162 1387 Planarity : 0.004 0.041 1452 Dihedral : 10.466 73.492 1474 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.92 % Allowed : 15.93 % Favored : 82.15 % 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: 0.84 (0.26), residues: 999 helix: 1.07 (0.24), residues: 471 sheet: 0.31 (0.53), residues: 86 loop : 0.20 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 555 TYR 0.018 0.001 TYR B 135 PHE 0.016 0.001 PHE A 652 TRP 0.008 0.001 TRP A 916 HIS 0.002 0.000 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 8867) covalent geometry : angle 0.46492 (12155) hydrogen bonds : bond 0.03370 ( 429) hydrogen bonds : angle 4.02907 ( 1147) metal coordination : bond 0.00823 ( 8) metal coordination : angle 2.14744 ( 6) Misc. bond : bond 0.00078 ( 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 145 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 0.334 Fit side-chains REVERT: A 158 ASN cc_start: 0.8016 (m110) cc_final: 0.7792 (m-40) REVERT: A 197 ARG cc_start: 0.7424 (ttp-170) cc_final: 0.7044 (ttp-170) REVERT: A 284 ASP cc_start: 0.8169 (OUTLIER) cc_final: 0.7955 (t70) REVERT: A 417 LYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7827 (tttm) REVERT: A 513 ARG cc_start: 0.7792 (ttm-80) cc_final: 0.7547 (ttm-80) REVERT: A 542 MET cc_start: 0.8090 (OUTLIER) cc_final: 0.7825 (mmm) REVERT: A 610 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7313 (mt-10) REVERT: A 796 GLU cc_start: 0.6969 (OUTLIER) cc_final: 0.6567 (mt-10) REVERT: A 885 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7019 (mp) REVERT: A 889 ARG cc_start: 0.7059 (mmm-85) cc_final: 0.6827 (mmm-85) REVERT: A 922 GLU cc_start: 0.7810 (tt0) cc_final: 0.7478 (tt0) REVERT: B 174 MET cc_start: 0.7867 (tpp) cc_final: 0.7581 (tpt) REVERT: C 23 GLU cc_start: 0.7706 (pt0) cc_final: 0.7441 (tt0) REVERT: C 62 MET cc_start: 0.6506 (ptp) cc_final: 0.6251 (ptp) outliers start: 17 outliers final: 3 residues processed: 136 average time/residue: 0.6331 time to fit residues: 91.2491 Evaluate side-chains 129 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 120 time to evaluate : 0.236 ------------------------------------------------------------------------------- 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 417 LYS 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 Chi-restraints excluded: chain C residue 22 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 28 optimal weight: 0.5980 chunk 101 optimal weight: 6.9990 chunk 89 optimal weight: 0.7980 chunk 57 optimal weight: 0.5980 chunk 86 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 52 optimal weight: 0.2980 chunk 56 optimal weight: 6.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 ASN ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 886 GLN C 34 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.164170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.119402 restraints weight = 8683.949| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 1.80 r_work: 0.3241 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3115 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3115 r_free = 0.3115 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3115 r_free = 0.3115 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3115 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2377 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= 0.095 Angle : 0.460 6.670 12161 Z= 0.245 Chirality : 0.038 0.141 1387 Planarity : 0.003 0.040 1452 Dihedral : 10.337 73.407 1474 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.13 % Allowed : 17.06 % Favored : 81.81 % 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: 1.02 (0.27), residues: 999 helix: 1.22 (0.25), residues: 471 sheet: 0.48 (0.55), residues: 86 loop : 0.26 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 555 TYR 0.016 0.001 TYR B 135 PHE 0.015 0.001 PHE A 652 TRP 0.010 0.001 TRP A 916 HIS 0.002 0.000 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00207 ( 8867) covalent geometry : angle 0.45822 (12155) hydrogen bonds : bond 0.03191 ( 429) hydrogen bonds : angle 3.94986 ( 1147) metal coordination : bond 0.00787 ( 8) metal coordination : angle 1.91915 ( 6) Misc. bond : bond 0.00068 ( 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 138 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 128 time to evaluate : 0.251 Fit side-chains REVERT: A 158 ASN cc_start: 0.8019 (m110) cc_final: 0.7792 (m-40) REVERT: A 197 ARG cc_start: 0.7440 (ttp-170) cc_final: 0.7059 (ttp-170) REVERT: A 284 ASP cc_start: 0.8186 (OUTLIER) cc_final: 0.7972 (t70) REVERT: A 542 MET cc_start: 0.8133 (OUTLIER) cc_final: 0.7830 (mmm) REVERT: A 610 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.7219 (mt-10) REVERT: A 796 GLU cc_start: 0.6959 (OUTLIER) cc_final: 0.6563 (mt-10) REVERT: A 885 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.6875 (mp) REVERT: A 922 GLU cc_start: 0.7794 (tt0) cc_final: 0.7475 (tt0) REVERT: B 174 MET cc_start: 0.7830 (tpp) cc_final: 0.7548 (tpt) REVERT: C 23 GLU cc_start: 0.7572 (pt0) cc_final: 0.7362 (tt0) REVERT: C 62 MET cc_start: 0.6494 (ptp) cc_final: 0.6232 (ptp) outliers start: 10 outliers final: 3 residues processed: 132 average time/residue: 0.6401 time to fit residues: 89.4062 Evaluate side-chains 129 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 121 time to evaluate : 0.214 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain C residue 22 VAL 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: 3.9990 chunk 43 optimal weight: 5.9990 chunk 96 optimal weight: 0.9990 chunk 7 optimal weight: 0.2980 chunk 30 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 45 optimal weight: 0.3980 chunk 61 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 552 ASN A 886 GLN C 34 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.166640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.123495 restraints weight = 9062.356| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 1.87 r_work: 0.3456 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3329 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3329 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8876 Z= 0.128 Angle : 0.493 7.811 12161 Z= 0.264 Chirality : 0.040 0.139 1387 Planarity : 0.003 0.040 1452 Dihedral : 10.437 73.414 1474 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.02 % Allowed : 17.06 % 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: 0.90 (0.26), residues: 999 helix: 1.10 (0.24), residues: 471 sheet: 0.49 (0.55), residues: 82 loop : 0.23 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 555 TYR 0.020 0.001 TYR A 289 PHE 0.018 0.001 PHE A 741 TRP 0.009 0.001 TRP A 916 HIS 0.003 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 8867) covalent geometry : angle 0.49129 (12155) hydrogen bonds : bond 0.03835 ( 429) hydrogen bonds : angle 4.05678 ( 1147) metal coordination : bond 0.01078 ( 8) metal coordination : angle 2.09411 ( 6) Misc. bond : bond 0.00100 ( 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 128 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 119 time to evaluate : 0.332 Fit side-chains REVERT: A 158 ASN cc_start: 0.8236 (m110) cc_final: 0.8029 (m-40) REVERT: A 284 ASP cc_start: 0.8271 (OUTLIER) cc_final: 0.8051 (t70) REVERT: A 332 LYS cc_start: 0.8064 (tttp) cc_final: 0.7714 (ttpt) REVERT: A 542 MET cc_start: 0.8385 (OUTLIER) cc_final: 0.8068 (mmm) REVERT: A 610 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7434 (mt-10) REVERT: A 796 GLU cc_start: 0.7094 (OUTLIER) cc_final: 0.6690 (mt-10) REVERT: A 885 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.7374 (mp) REVERT: A 922 GLU cc_start: 0.8028 (tt0) cc_final: 0.7817 (tt0) REVERT: B 174 MET cc_start: 0.7889 (tpp) cc_final: 0.7585 (tpt) REVERT: C 23 GLU cc_start: 0.7788 (pt0) cc_final: 0.7531 (tt0) REVERT: C 62 MET cc_start: 0.6421 (ptp) cc_final: 0.6182 (ptp) outliers start: 9 outliers final: 2 residues processed: 122 average time/residue: 0.6436 time to fit residues: 83.2061 Evaluate side-chains 124 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 117 time to evaluate : 0.302 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain C residue 22 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 7 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 94 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 100 optimal weight: 8.9990 chunk 73 optimal weight: 4.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 886 GLN C 34 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.167146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.124137 restraints weight = 9044.908| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 1.87 r_work: 0.3466 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3342 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3342 r_free = 0.3342 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3342 r_free = 0.3342 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3342 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8876 Z= 0.118 Angle : 0.491 7.945 12161 Z= 0.261 Chirality : 0.039 0.139 1387 Planarity : 0.003 0.040 1452 Dihedral : 10.410 73.429 1474 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.02 % Allowed : 17.06 % 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: 0.92 (0.27), residues: 999 helix: 1.12 (0.24), residues: 471 sheet: 0.52 (0.55), residues: 82 loop : 0.22 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 555 TYR 0.018 0.001 TYR A 289 PHE 0.017 0.001 PHE A 741 TRP 0.010 0.001 TRP A 916 HIS 0.003 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 8867) covalent geometry : angle 0.48891 (12155) hydrogen bonds : bond 0.03650 ( 429) hydrogen bonds : angle 4.04223 ( 1147) metal coordination : bond 0.00901 ( 8) metal coordination : angle 2.05157 ( 6) Misc. bond : bond 0.00092 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3581.15 seconds wall clock time: 61 minutes 29.01 seconds (3689.01 seconds total)