Starting phenix.real_space_refine on Sat Oct 11 19:14:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6d6v_7821/10_2025/6d6v_7821.cif Found real_map, /net/cci-nas-00/data/ceres_data/6d6v_7821/10_2025/6d6v_7821.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6d6v_7821/10_2025/6d6v_7821.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6d6v_7821/10_2025/6d6v_7821.map" model { file = "/net/cci-nas-00/data/ceres_data/6d6v_7821/10_2025/6d6v_7821.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6d6v_7821/10_2025/6d6v_7821.cif" } resolution = 4.8 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 ------------------------------------------------------------------------------- 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= 0.006 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 177 5.49 5 S 54 5.16 5 C 10405 2.51 5 N 2948 2.21 5 O 3732 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17317 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 8253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 980, 8253 Classifications: {'peptide': 980} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 20, 'TRANS': 959} Chain breaks: 4 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "D" Number of atoms: 1538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1538 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 3, 'TRANS': 181} Chain: "F" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 919 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "E" Number of atoms: 1207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1207 Classifications: {'peptide': 149} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 143} Chain: "B" Number of atoms: 3322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 3322 Classifications: {'RNA': 159} Modifications used: {'5*END': 1, 'rna2p_pur': 18, 'rna2p_pyr': 21, 'rna3p_pur': 59, 'rna3p_pyr': 60} Link IDs: {'rna2p': 38, 'rna3p': 120} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {' U%rna3p_pyr:plan': 1, ' G%rna3p_pur:plan': 2, ' G%rna3p_pur:plan2': 2} Unresolved non-hydrogen planarities: 34 Chain: "C" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 406 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "G" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 785 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 157} Link IDs: {'TRANS': 156} Unresolved non-hydrogen bonds: 314 Unresolved non-hydrogen angles: 471 Unresolved non-hydrogen dihedrals: 157 Planarities with less than four sites: {'UNK:plan-1': 157} Unresolved non-hydrogen planarities: 157 Chain: "H" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 886 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 105} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 8788 SG CYS D 575 71.318 62.077 84.962 1.00328.59 S Time building chain proxies: 3.47, per 1000 atoms: 0.20 Number of scatterers: 17317 At special positions: 0 Unit cell: (148.24, 160.48, 114.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 54 16.00 P 177 15.00 O 3732 8.00 N 2948 7.00 C 10405 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.63 Conformation dependent library (CDL) restraints added in 577.3 milliseconds Enol-peptide restraints added in 238.4 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 801 " pdb="ZN ZN D 801 " - pdb=" SG CYS D 575 " 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3282 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 13 sheets defined 51.5% alpha, 13.6% beta 43 base pairs and 78 stacking pairs defined. Time for finding SS restraints: 2.40 Creating SS restraints... Processing helix chain 'A' and resid 19 through 26 Processing helix chain 'A' and resid 36 through 43 Processing helix chain 'A' and resid 53 through 63 Processing helix chain 'A' and resid 71 through 76 Processing helix chain 'A' and resid 88 through 99 Processing helix chain 'A' and resid 106 through 110 Processing helix chain 'A' and resid 125 through 131 removed outlier: 3.583A pdb=" N GLN A 129 " --> pdb=" O ASN A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 144 Processing helix chain 'A' and resid 144 through 155 Processing helix chain 'A' and resid 173 through 178 removed outlier: 3.751A pdb=" N TYR A 177 " --> pdb=" O CYS A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 230 Processing helix chain 'A' and resid 301 through 320 Processing helix chain 'A' and resid 323 through 331 Processing helix chain 'A' and resid 336 through 351 Processing helix chain 'A' and resid 355 through 368 Processing helix chain 'A' and resid 372 through 386 Processing helix chain 'A' and resid 389 through 394 Processing helix chain 'A' and resid 394 through 411 removed outlier: 4.371A pdb=" N TYR A 406 " --> pdb=" O LEU A 402 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU A 407 " --> pdb=" O GLU A 403 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N MET A 411 " --> pdb=" O GLU A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 424 Processing helix chain 'A' and resid 436 through 443 removed outlier: 3.679A pdb=" N ASN A 439 " --> pdb=" O ASP A 436 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN A 440 " --> pdb=" O LEU A 437 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N LYS A 441 " --> pdb=" O LYS A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 467 Processing helix chain 'A' and resid 467 through 475 Processing helix chain 'A' and resid 493 through 505 Processing helix chain 'A' and resid 506 through 509 removed outlier: 4.321A pdb=" N GLU A 509 " --> pdb=" O LYS A 506 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 506 through 509' Processing helix chain 'A' and resid 551 through 579 removed outlier: 3.670A pdb=" N LYS A 555 " --> pdb=" O LYS A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 607 Processing helix chain 'A' and resid 627 through 636 Processing helix chain 'A' and resid 711 through 717 removed outlier: 3.970A pdb=" N LEU A 715 " --> pdb=" O ASP A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 753 removed outlier: 3.836A pdb=" N ILE A 745 " --> pdb=" O THR A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 805 removed outlier: 3.686A pdb=" N GLU A 792 " --> pdb=" O LYS A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 823 through 840 Processing helix chain 'A' and resid 856 through 865 Processing helix chain 'A' and resid 894 through 900 Processing helix chain 'A' and resid 911 through 921 removed outlier: 4.249A pdb=" N ASN A 918 " --> pdb=" O SER A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 965 removed outlier: 3.639A pdb=" N LEU A 942 " --> pdb=" O SER A 938 " (cutoff:3.500A) Proline residue: A 959 - end of helix Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 974 through 980 Processing helix chain 'A' and resid 983 through 1003 removed outlier: 3.750A pdb=" N ASN A 987 " --> pdb=" O ASN A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1040 Processing helix chain 'A' and resid 1043 through 1075 removed outlier: 4.742A pdb=" N LYS A1049 " --> pdb=" O GLY A1045 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LEU A1069 " --> pdb=" O GLY A1065 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLN A1070 " --> pdb=" O CYS A1066 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN A1075 " --> pdb=" O LEU A1071 " (cutoff:3.500A) Processing helix chain 'A' and resid 1082 through 1093 Processing helix chain 'A' and resid 1099 through 1108 Proline residue: A1105 - end of helix Processing helix chain 'D' and resid 516 through 526 Processing helix chain 'D' and resid 604 through 613 Processing helix chain 'D' and resid 619 through 621 No H-bonds generated for 'chain 'D' and resid 619 through 621' Processing helix chain 'D' and resid 622 through 634 Processing helix chain 'D' and resid 635 through 646 removed outlier: 3.602A pdb=" N LEU D 646 " --> pdb=" O LEU D 642 " (cutoff:3.500A) Processing helix chain 'D' and resid 680 through 693 removed outlier: 3.816A pdb=" N SER D 684 " --> pdb=" O ILE D 680 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 21 removed outlier: 5.904A pdb=" N ALA F 19 " --> pdb=" O GLU F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 110 removed outlier: 3.534A pdb=" N TYR F 102 " --> pdb=" O ASP F 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 49 removed outlier: 3.781A pdb=" N ILE E 39 " --> pdb=" O ASN E 35 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN E 41 " --> pdb=" O PHE E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 120 removed outlier: 5.566A pdb=" N GLU E 117 " --> pdb=" O VAL E 113 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ILE E 118 " --> pdb=" O GLN E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 175 removed outlier: 3.920A pdb=" N ILE E 156 " --> pdb=" O ASP E 152 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 28 removed outlier: 3.896A pdb=" N UNK G 11 " --> pdb=" O UNK G 7 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N UNK G 13 " --> pdb=" O UNK G 9 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N UNK G 14 " --> pdb=" O UNK G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 72 removed outlier: 4.133A pdb=" N UNK G 71 " --> pdb=" O UNK G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 126 through 133 removed outlier: 3.627A pdb=" N UNK G 130 " --> pdb=" O UNK G 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 154 Processing helix chain 'H' and resid 391 through 401 removed outlier: 3.501A pdb=" N VAL H 395 " --> pdb=" O LEU H 391 " (cutoff:3.500A) Processing helix chain 'H' and resid 468 through 479 Processing helix chain 'H' and resid 503 through 531 removed outlier: 4.041A pdb=" N PHE H 525 " --> pdb=" O PHE H 521 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN H 530 " --> pdb=" O PHE H 526 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 35 Processing sheet with id=AA2, first strand: chain 'A' and resid 157 through 162 removed outlier: 7.938A pdb=" N PHE A 158 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL A 169 " --> pdb=" O PHE A 158 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N LYS A 160 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N LEU A 167 " --> pdb=" O LYS A 160 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 476 through 481 removed outlier: 4.615A pdb=" N LYS A 481 " --> pdb=" O GLN A 487 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N GLN A 487 " --> pdb=" O LYS A 481 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 532 through 534 Processing sheet with id=AA5, first strand: chain 'A' and resid 613 through 618 Processing sheet with id=AA6, first strand: chain 'A' and resid 647 through 648 removed outlier: 4.202A pdb=" N ILE A 647 " --> pdb=" O ASN A 733 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 880 through 882 Processing sheet with id=AA8, first strand: chain 'D' and resid 551 through 554 removed outlier: 4.885A pdb=" N TYR D 670 " --> pdb=" O PRO D 599 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N MET D 601 " --> pdb=" O TYR D 670 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N PHE D 603 " --> pdb=" O VAL D 672 " (cutoff:3.500A) removed outlier: 8.906A pdb=" N LYS D 674 " --> pdb=" O PHE D 603 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N TYR D 670 " --> pdb=" O GLU D 658 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N GLU D 658 " --> pdb=" O TYR D 670 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N VAL D 672 " --> pdb=" O GLN D 656 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N GLN D 656 " --> pdb=" O VAL D 672 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 562 through 563 removed outlier: 3.671A pdb=" N PHE D 571 " --> pdb=" O LEU D 563 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 70 through 75 removed outlier: 6.670A pdb=" N ILE F 43 " --> pdb=" O CYS F 33 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU F 44 " --> pdb=" O VAL F 54 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N VAL F 83 " --> pdb=" O HIS F 53 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N VAL F 55 " --> pdb=" O VAL F 83 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 31 through 33 removed outlier: 3.553A pdb=" N TYR E 146 " --> pdb=" O MET E 133 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LYS E 135 " --> pdb=" O LEU E 144 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N LEU E 144 " --> pdb=" O LYS E 135 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N LEU E 144 " --> pdb=" O GLU E 97 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL E 99 " --> pdb=" O LEU E 144 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N TYR E 146 " --> pdb=" O VAL E 99 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY E 94 " --> pdb=" O ASP E 91 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ILE E 85 " --> pdb=" O ILE E 100 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N MET E 86 " --> pdb=" O LEU E 76 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LEU E 76 " --> pdb=" O MET E 86 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LYS E 88 " --> pdb=" O GLU E 74 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 87 through 89 Processing sheet with id=AB4, first strand: chain 'H' and resid 406 through 411 removed outlier: 4.766A pdb=" N LEU H 487 " --> pdb=" O VAL H 498 " (cutoff:3.500A) 630 hydrogen bonds defined for protein. 1806 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 103 hydrogen bonds 194 hydrogen bond angles 0 basepair planarities 43 basepair parallelities 78 stacking parallelities Total time for adding SS restraints: 3.18 Time building geometry restraints manager: 2.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.34: 5118 1.34 - 1.49: 6588 1.49 - 1.65: 6213 1.65 - 1.80: 63 1.80 - 1.95: 16 Bond restraints: 17998 Sorted by residual: bond pdb=" CA SER A 890 " pdb=" C SER A 890 " ideal model delta sigma weight residual 1.524 1.473 0.051 7.00e-03 2.04e+04 5.30e+01 bond pdb=" SD MET H 527 " pdb=" CE MET H 527 " ideal model delta sigma weight residual 1.791 1.952 -0.161 2.50e-02 1.60e+03 4.17e+01 bond pdb=" CG MET H 527 " pdb=" SD MET H 527 " ideal model delta sigma weight residual 1.803 1.955 -0.152 2.50e-02 1.60e+03 3.69e+01 bond pdb=" CB ASN A 648 " pdb=" CG ASN A 648 " ideal model delta sigma weight residual 1.516 1.399 0.117 2.50e-02 1.60e+03 2.21e+01 bond pdb=" CA LEU A 923 " pdb=" C LEU A 923 " ideal model delta sigma weight residual 1.523 1.440 0.083 1.80e-02 3.09e+03 2.13e+01 ... (remaining 17993 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.51: 23913 3.51 - 7.02: 1020 7.02 - 10.52: 138 10.52 - 14.03: 33 14.03 - 17.54: 8 Bond angle restraints: 25112 Sorted by residual: angle pdb=" N ILE A 626 " pdb=" CA ILE A 626 " pdb=" C ILE A 626 " ideal model delta sigma weight residual 108.84 120.25 -11.41 1.32e+00 5.74e-01 7.47e+01 angle pdb=" C SER A 922 " pdb=" N LEU A 923 " pdb=" CA LEU A 923 " ideal model delta sigma weight residual 122.31 138.67 -16.36 2.00e+00 2.50e-01 6.69e+01 angle pdb=" N LYS A 849 " pdb=" CA LYS A 849 " pdb=" C LYS A 849 " ideal model delta sigma weight residual 108.07 118.55 -10.48 1.38e+00 5.25e-01 5.77e+01 angle pdb=" N ASP A 627 " pdb=" CA ASP A 627 " pdb=" C ASP A 627 " ideal model delta sigma weight residual 107.73 96.14 11.59 1.80e+00 3.09e-01 4.15e+01 angle pdb=" CA PRO A 934 " pdb=" C PRO A 934 " pdb=" N ASN A 935 " ideal model delta sigma weight residual 117.98 109.19 8.79 1.43e+00 4.89e-01 3.78e+01 ... (remaining 25107 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.72: 10228 35.72 - 71.44: 620 71.44 - 107.16: 88 107.16 - 142.88: 12 142.88 - 178.61: 10 Dihedral angle restraints: 10958 sinusoidal: 5916 harmonic: 5042 Sorted by residual: dihedral pdb=" CA SER A 299 " pdb=" C SER A 299 " pdb=" N CYS A 300 " pdb=" CA CYS A 300 " ideal model delta harmonic sigma weight residual -180.00 -113.29 -66.71 0 5.00e+00 4.00e-02 1.78e+02 dihedral pdb=" CA UNK G 62 " pdb=" C UNK G 62 " pdb=" N UNK G 63 " pdb=" CA UNK G 63 " ideal model delta harmonic sigma weight residual -180.00 -130.09 -49.91 0 5.00e+00 4.00e-02 9.97e+01 dihedral pdb=" CA PHE F 97 " pdb=" C PHE F 97 " pdb=" N ASP F 98 " pdb=" CA ASP F 98 " ideal model delta harmonic sigma weight residual 180.00 131.55 48.45 0 5.00e+00 4.00e-02 9.39e+01 ... (remaining 10955 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.200: 2854 0.200 - 0.400: 62 0.400 - 0.600: 6 0.600 - 0.800: 2 0.800 - 1.000: 1 Chirality restraints: 2925 Sorted by residual: chirality pdb=" C1' C B 46 " pdb=" O4' C B 46 " pdb=" C2' C B 46 " pdb=" N1 C B 46 " both_signs ideal model delta sigma weight residual False 2.46 1.46 1.00 2.00e-01 2.50e+01 2.50e+01 chirality pdb=" CG LEU A 565 " pdb=" CB LEU A 565 " pdb=" CD1 LEU A 565 " pdb=" CD2 LEU A 565 " both_signs ideal model delta sigma weight residual False -2.59 -1.81 -0.78 2.00e-01 2.50e+01 1.53e+01 chirality pdb=" C3' U B 42 " pdb=" C4' U B 42 " pdb=" O3' U B 42 " pdb=" C2' U B 42 " both_signs ideal model delta sigma weight residual False -2.48 -1.79 -0.69 2.00e-01 2.50e+01 1.18e+01 ... (remaining 2922 not shown) Planarity restraints: 2584 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 585 " 0.053 2.00e-02 2.50e+03 3.15e-02 1.99e+01 pdb=" CG TYR A 585 " -0.070 2.00e-02 2.50e+03 pdb=" CD1 TYR A 585 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR A 585 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR A 585 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR A 585 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR A 585 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 585 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT C 15 " 0.059 2.00e-02 2.50e+03 2.82e-02 1.99e+01 pdb=" N1 DT C 15 " -0.029 2.00e-02 2.50e+03 pdb=" C2 DT C 15 " 0.011 2.00e-02 2.50e+03 pdb=" O2 DT C 15 " -0.030 2.00e-02 2.50e+03 pdb=" N3 DT C 15 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DT C 15 " 0.012 2.00e-02 2.50e+03 pdb=" O4 DT C 15 " 0.020 2.00e-02 2.50e+03 pdb=" C5 DT C 15 " 0.001 2.00e-02 2.50e+03 pdb=" C7 DT C 15 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DT C 15 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C B 46 " -0.056 2.00e-02 2.50e+03 2.93e-02 1.93e+01 pdb=" N1 C B 46 " 0.050 2.00e-02 2.50e+03 pdb=" C2 C B 46 " 0.038 2.00e-02 2.50e+03 pdb=" O2 C B 46 " -0.007 2.00e-02 2.50e+03 pdb=" N3 C B 46 " -0.010 2.00e-02 2.50e+03 pdb=" C4 C B 46 " -0.008 2.00e-02 2.50e+03 pdb=" N4 C B 46 " -0.019 2.00e-02 2.50e+03 pdb=" C5 C B 46 " 0.003 2.00e-02 2.50e+03 pdb=" C6 C B 46 " 0.009 2.00e-02 2.50e+03 ... (remaining 2581 not shown) Histogram of nonbonded interaction distances: 1.19 - 1.93: 8 1.93 - 2.67: 1148 2.67 - 3.42: 26487 3.42 - 4.16: 48918 4.16 - 4.90: 75700 Nonbonded interactions: 152261 Sorted by model distance: nonbonded pdb=" OP2 G B 121 " pdb=" O LYS H 518 " model vdw 1.189 3.040 nonbonded pdb=" C5' G B 121 " pdb=" CB PHE H 521 " model vdw 1.441 3.840 nonbonded pdb=" O4' G B 121 " pdb=" O LYS H 517 " model vdw 1.447 3.040 nonbonded pdb=" CB UNK G 51 " pdb=" O UNK G 73 " model vdw 1.641 3.440 nonbonded pdb=" OE2 GLU E 65 " pdb=" O MET E 136 " model vdw 1.673 3.040 ... (remaining 152256 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 19.200 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 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 : 0.013 0.233 17999 Z= 0.665 Angle : 1.698 17.540 25112 Z= 0.888 Chirality : 0.085 1.000 2925 Planarity : 0.010 0.091 2584 Dihedral : 21.411 178.605 7676 Min Nonbonded Distance : 1.189 Molprobity Statistics. All-atom Clashscore : 25.73 Ramachandran Plot: Outliers : 0.73 % Allowed : 15.78 % Favored : 83.50 % Rotamer: Outliers : 0.97 % Allowed : 4.04 % Favored : 94.99 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 6.25 % Twisted General : 2.14 % 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 aren not related in a simple way. whole: -4.28 (0.17), residues: 1515 helix: -2.30 (0.15), residues: 637 sheet: -2.50 (0.40), residues: 138 loop : -3.45 (0.20), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.002 ARG A 727 TYR 0.070 0.006 TYR A 585 PHE 0.073 0.006 PHE A 634 TRP 0.018 0.004 TRP A1030 HIS 0.015 0.004 HIS A 319 Details of bonding type rmsd covalent geometry : bond 0.01327 (17998) covalent geometry : angle 1.69761 (25112) hydrogen bonds : bond 0.20647 ( 733) hydrogen bonds : angle 8.33635 ( 2000) metal coordination : bond 0.23275 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 560 ASN cc_start: 0.8434 (m-40) cc_final: 0.8017 (m-40) REVERT: A 566 MET cc_start: 0.8902 (mmt) cc_final: 0.8675 (tpp) REVERT: A 631 LEU cc_start: 0.9389 (OUTLIER) cc_final: 0.9180 (mt) REVERT: A 634 PHE cc_start: 0.8421 (OUTLIER) cc_final: 0.8099 (m-10) REVERT: A 701 ARG cc_start: 0.7806 (ptm160) cc_final: 0.7291 (ptt-90) REVERT: A 777 ILE cc_start: 0.9473 (pt) cc_final: 0.8942 (pt) REVERT: A 955 MET cc_start: 0.9326 (mtt) cc_final: 0.9120 (mmp) REVERT: D 586 MET cc_start: 0.6292 (tpp) cc_final: 0.6010 (tpp) REVERT: D 601 MET cc_start: 0.8037 (mtt) cc_final: 0.7479 (mtp) REVERT: H 397 LEU cc_start: 0.8459 (tp) cc_final: 0.8123 (pp) outliers start: 14 outliers final: 8 residues processed: 137 average time/residue: 0.1508 time to fit residues: 30.3991 Evaluate side-chains 89 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.1980 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 10.0000 overall best weight: 1.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN A 105 ASN A 141 ASN ** A 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 248 ASN A 319 HIS ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 GLN A 475 ASN ** A 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 569 GLN A 590 ASN A 633 ASN A 648 ASN ** A 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 697 ASN A 702 GLN ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 824 GLN A 839 ASN A 896 GLN A 918 ASN A 927 GLN ** A 945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1016 ASN A1098 GLN ** D 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 79 ASN F 110 GLN ** E 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 143 GLN ** H 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 482 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.046769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.034963 restraints weight = 212467.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.035846 restraints weight = 139928.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.036601 restraints weight = 104091.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.037052 restraints weight = 83361.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.037329 restraints weight = 71102.485| |-----------------------------------------------------------------------------| r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 17999 Z= 0.183 Angle : 0.887 18.986 25112 Z= 0.460 Chirality : 0.051 0.926 2925 Planarity : 0.005 0.068 2584 Dihedral : 25.079 171.126 4350 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 20.39 Ramachandran Plot: Outliers : 0.13 % Allowed : 12.67 % Favored : 87.19 % Rotamer: Outliers : 0.07 % Allowed : 2.57 % Favored : 97.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.87 % 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 aren not related in a simple way. whole: -2.95 (0.20), residues: 1515 helix: -0.84 (0.19), residues: 648 sheet: -2.04 (0.41), residues: 155 loop : -3.07 (0.21), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 534 TYR 0.029 0.002 TYR A1061 PHE 0.044 0.002 PHE A 634 TRP 0.037 0.003 TRP A 604 HIS 0.006 0.002 HIS A 234 Details of bonding type rmsd covalent geometry : bond 0.00362 (17998) covalent geometry : angle 0.88715 (25112) hydrogen bonds : bond 0.06514 ( 733) hydrogen bonds : angle 6.27057 ( 2000) metal coordination : bond 0.00478 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 139 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 THR cc_start: 0.8448 (m) cc_final: 0.8100 (p) REVERT: A 139 LEU cc_start: 0.9694 (mt) cc_final: 0.9385 (mt) REVERT: A 565 LEU cc_start: 0.9642 (mm) cc_final: 0.9415 (mm) REVERT: A 701 ARG cc_start: 0.7382 (ptm160) cc_final: 0.7012 (mtm180) REVERT: A 811 MET cc_start: 0.8748 (tmm) cc_final: 0.8261 (ppp) REVERT: A 912 LEU cc_start: 0.9294 (tp) cc_final: 0.8858 (tp) REVERT: A 1029 MET cc_start: 0.8941 (mmp) cc_final: 0.8669 (mmp) REVERT: D 586 MET cc_start: 0.6823 (tpp) cc_final: 0.6200 (tpp) REVERT: D 601 MET cc_start: 0.8748 (mtt) cc_final: 0.8291 (ttm) REVERT: F 59 TYR cc_start: 0.8995 (t80) cc_final: 0.8501 (t80) REVERT: F 61 ARG cc_start: 0.8380 (ttt-90) cc_final: 0.7488 (tmm160) REVERT: E 117 GLU cc_start: 0.8583 (mm-30) cc_final: 0.8321 (mt-10) REVERT: E 146 TYR cc_start: 0.9152 (t80) cc_final: 0.8046 (t80) REVERT: E 162 ASP cc_start: 0.9418 (m-30) cc_final: 0.9083 (m-30) outliers start: 1 outliers final: 1 residues processed: 139 average time/residue: 0.1456 time to fit residues: 30.1353 Evaluate side-chains 83 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 82 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 72 optimal weight: 0.6980 chunk 162 optimal weight: 20.0000 chunk 181 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 146 optimal weight: 10.0000 chunk 91 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 51 optimal weight: 7.9990 chunk 147 optimal weight: 30.0000 chunk 129 optimal weight: 0.0470 overall best weight: 3.1484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN ** A 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 ASN ** A 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 574 ASN ** A 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 747 ASN ** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 ASN A 900 ASN ** A 945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 949 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 983 ASN ** A1014 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.045947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.034129 restraints weight = 219464.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.034971 restraints weight = 145410.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.035673 restraints weight = 108773.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.036137 restraints weight = 87676.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.036485 restraints weight = 75189.113| |-----------------------------------------------------------------------------| r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 17999 Z= 0.206 Angle : 0.860 18.201 25112 Z= 0.447 Chirality : 0.050 0.966 2925 Planarity : 0.005 0.062 2584 Dihedral : 24.770 171.234 4350 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 22.03 Ramachandran Plot: Outliers : 0.13 % Allowed : 14.65 % Favored : 85.21 % Rotamer: Outliers : 0.14 % Allowed : 3.48 % Favored : 96.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.87 % 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 aren not related in a simple way. whole: -2.53 (0.20), residues: 1515 helix: -0.42 (0.19), residues: 656 sheet: -1.97 (0.42), residues: 137 loop : -2.89 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 128 TYR 0.037 0.002 TYR D 565 PHE 0.050 0.002 PHE A 634 TRP 0.037 0.002 TRP A 604 HIS 0.007 0.001 HIS A 234 Details of bonding type rmsd covalent geometry : bond 0.00415 (17998) covalent geometry : angle 0.85973 (25112) hydrogen bonds : bond 0.06280 ( 733) hydrogen bonds : angle 5.92774 ( 2000) metal coordination : bond 0.00201 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 112 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 LEU cc_start: 0.9697 (mt) cc_final: 0.9416 (mt) REVERT: A 566 MET cc_start: 0.8936 (tpt) cc_final: 0.8277 (tpt) REVERT: A 593 ILE cc_start: 0.9374 (tt) cc_final: 0.8943 (mt) REVERT: A 634 PHE cc_start: 0.8569 (m-10) cc_final: 0.8243 (m-10) REVERT: A 701 ARG cc_start: 0.7436 (ptm160) cc_final: 0.7233 (mtm180) REVERT: A 811 MET cc_start: 0.8835 (tmm) cc_final: 0.8322 (ppp) REVERT: A 912 LEU cc_start: 0.9472 (tp) cc_final: 0.9095 (tp) REVERT: A 1029 MET cc_start: 0.9105 (mmp) cc_final: 0.8795 (mmm) REVERT: D 586 MET cc_start: 0.6691 (tpp) cc_final: 0.5951 (tpp) REVERT: F 59 TYR cc_start: 0.9067 (t80) cc_final: 0.8630 (t80) REVERT: F 61 ARG cc_start: 0.8617 (ttt-90) cc_final: 0.7728 (tmm160) REVERT: E 86 MET cc_start: 0.8418 (tpt) cc_final: 0.8033 (tpp) REVERT: E 117 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8200 (mt-10) REVERT: E 136 MET cc_start: 0.9182 (mmp) cc_final: 0.8848 (mmm) REVERT: E 146 TYR cc_start: 0.9155 (t80) cc_final: 0.8405 (t80) REVERT: E 162 ASP cc_start: 0.9363 (m-30) cc_final: 0.8981 (m-30) outliers start: 2 outliers final: 1 residues processed: 114 average time/residue: 0.1344 time to fit residues: 23.7287 Evaluate side-chains 82 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 81 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 43 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 95 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 165 optimal weight: 40.0000 chunk 38 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 HIS ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 569 GLN ** A 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 ASN A 824 GLN A 853 ASN A 904 ASN A 918 ASN ** A 945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 949 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 461 GLN ** H 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.047074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.035128 restraints weight = 214831.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.036015 restraints weight = 142607.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.036749 restraints weight = 106230.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.037238 restraints weight = 85616.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.037603 restraints weight = 73142.359| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17999 Z= 0.157 Angle : 0.768 17.705 25112 Z= 0.398 Chirality : 0.048 0.989 2925 Planarity : 0.004 0.068 2584 Dihedral : 24.450 171.324 4350 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 19.05 Ramachandran Plot: Outliers : 0.07 % Allowed : 12.81 % Favored : 87.13 % Rotamer: Outliers : 0.14 % Allowed : 1.67 % Favored : 98.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.40 % 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 aren not related in a simple way. whole: -2.16 (0.21), residues: 1515 helix: 0.02 (0.20), residues: 661 sheet: -1.89 (0.43), residues: 131 loop : -2.83 (0.22), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 812 TYR 0.032 0.002 TYR D 565 PHE 0.039 0.002 PHE A 634 TRP 0.042 0.002 TRP A 604 HIS 0.004 0.001 HIS E 53 Details of bonding type rmsd covalent geometry : bond 0.00312 (17998) covalent geometry : angle 0.76780 (25112) hydrogen bonds : bond 0.05456 ( 733) hydrogen bonds : angle 5.61916 ( 2000) metal coordination : bond 0.00091 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 115 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 THR cc_start: 0.8341 (m) cc_final: 0.8124 (p) REVERT: A 139 LEU cc_start: 0.9718 (mt) cc_final: 0.9373 (mt) REVERT: A 562 ASN cc_start: 0.8289 (t0) cc_final: 0.7869 (t0) REVERT: A 569 GLN cc_start: 0.9465 (tt0) cc_final: 0.8579 (tp-100) REVERT: A 701 ARG cc_start: 0.7408 (ptm160) cc_final: 0.7027 (mtm180) REVERT: A 811 MET cc_start: 0.8838 (tmm) cc_final: 0.8300 (ppp) REVERT: A 910 LYS cc_start: 0.9039 (mtpt) cc_final: 0.8798 (mmmt) REVERT: A 1029 MET cc_start: 0.9175 (mmp) cc_final: 0.8848 (mmp) REVERT: D 586 MET cc_start: 0.6870 (tpp) cc_final: 0.5957 (tpp) REVERT: F 18 MET cc_start: 0.9582 (mmp) cc_final: 0.9313 (mmm) REVERT: F 59 TYR cc_start: 0.9080 (t80) cc_final: 0.8643 (t80) REVERT: F 61 ARG cc_start: 0.8490 (ttt-90) cc_final: 0.7749 (tmm160) REVERT: E 86 MET cc_start: 0.8344 (tpt) cc_final: 0.7886 (tpp) REVERT: E 146 TYR cc_start: 0.9185 (t80) cc_final: 0.8478 (t80) REVERT: E 162 ASP cc_start: 0.9311 (m-30) cc_final: 0.8911 (m-30) outliers start: 2 outliers final: 0 residues processed: 116 average time/residue: 0.1402 time to fit residues: 25.0690 Evaluate side-chains 88 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 44 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 110 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 chunk 112 optimal weight: 8.9990 chunk 76 optimal weight: 6.9990 chunk 36 optimal weight: 9.9990 chunk 74 optimal weight: 0.0170 chunk 88 optimal weight: 4.9990 overall best weight: 1.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 GLN ** A 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 865 HIS ** A 945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1014 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 472 GLN ** 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 = 0.3403 r_free = 0.3403 target = 0.047692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.035659 restraints weight = 212210.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.036501 restraints weight = 142758.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.037230 restraints weight = 107440.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.037685 restraints weight = 87219.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 71)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.038076 restraints weight = 74966.624| |-----------------------------------------------------------------------------| r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.4362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17999 Z= 0.142 Angle : 0.734 17.539 25112 Z= 0.381 Chirality : 0.047 0.995 2925 Planarity : 0.004 0.062 2584 Dihedral : 24.175 171.994 4350 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 17.69 Ramachandran Plot: Outliers : 0.07 % Allowed : 12.54 % Favored : 87.39 % Rotamer: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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 aren not related in a simple way. whole: -1.88 (0.21), residues: 1515 helix: 0.27 (0.20), residues: 658 sheet: -1.49 (0.44), residues: 133 loop : -2.74 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 812 TYR 0.028 0.002 TYR D 565 PHE 0.039 0.002 PHE A 634 TRP 0.043 0.002 TRP A 604 HIS 0.012 0.001 HIS A 234 Details of bonding type rmsd covalent geometry : bond 0.00285 (17998) covalent geometry : angle 0.73437 (25112) hydrogen bonds : bond 0.05106 ( 733) hydrogen bonds : angle 5.38628 ( 2000) metal coordination : bond 0.00092 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 LEU cc_start: 0.9710 (mt) cc_final: 0.9388 (mt) REVERT: A 562 ASN cc_start: 0.8330 (t0) cc_final: 0.7442 (m-40) REVERT: A 569 GLN cc_start: 0.9469 (tt0) cc_final: 0.8674 (tp-100) REVERT: A 701 ARG cc_start: 0.7105 (ptm160) cc_final: 0.6773 (mtt180) REVERT: A 811 MET cc_start: 0.8727 (tmm) cc_final: 0.8143 (ppp) REVERT: A 910 LYS cc_start: 0.9052 (mtpt) cc_final: 0.8790 (mmmt) REVERT: A 955 MET cc_start: 0.9473 (mmm) cc_final: 0.8946 (mmm) REVERT: A 1029 MET cc_start: 0.9197 (mmp) cc_final: 0.8978 (mmm) REVERT: D 586 MET cc_start: 0.6734 (tpp) cc_final: 0.5951 (tpp) REVERT: F 59 TYR cc_start: 0.9056 (t80) cc_final: 0.8797 (t80) REVERT: E 86 MET cc_start: 0.8525 (tpt) cc_final: 0.7991 (tpp) REVERT: E 136 MET cc_start: 0.9132 (mmp) cc_final: 0.8800 (mmm) REVERT: E 146 TYR cc_start: 0.9221 (t80) cc_final: 0.8539 (t80) REVERT: E 162 ASP cc_start: 0.9083 (m-30) cc_final: 0.8797 (m-30) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.1423 time to fit residues: 25.3696 Evaluate side-chains 82 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 1 optimal weight: 10.0000 chunk 130 optimal weight: 8.9990 chunk 128 optimal weight: 1.9990 chunk 21 optimal weight: 9.9990 chunk 160 optimal weight: 40.0000 chunk 91 optimal weight: 7.9990 chunk 174 optimal weight: 9.9990 chunk 16 optimal weight: 7.9990 chunk 48 optimal weight: 0.4980 chunk 150 optimal weight: 20.0000 chunk 36 optimal weight: 10.0000 overall best weight: 5.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN A 175 ASN A 317 ASN ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 GLN A 361 ASN ** A 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 702 GLN ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 ASN A 839 ASN ** A 840 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1014 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 659 ASN F 110 GLN ** E 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 172 HIS ** H 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.045013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.033225 restraints weight = 218940.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.034032 restraints weight = 148001.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.034718 restraints weight = 111794.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.035136 restraints weight = 90804.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 70)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.035504 restraints weight = 78071.495| |-----------------------------------------------------------------------------| r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.4211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 17999 Z= 0.278 Angle : 0.888 18.284 25112 Z= 0.460 Chirality : 0.050 0.935 2925 Planarity : 0.005 0.055 2584 Dihedral : 24.526 170.870 4350 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 28.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 14.06 % Favored : 85.87 % Rotamer: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.47 % 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 aren not related in a simple way. whole: -2.32 (0.21), residues: 1515 helix: -0.19 (0.19), residues: 658 sheet: -2.40 (0.39), residues: 155 loop : -2.71 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 727 TYR 0.027 0.002 TYR D 565 PHE 0.033 0.003 PHE A 819 TRP 0.041 0.003 TRP A 604 HIS 0.008 0.002 HIS A 234 Details of bonding type rmsd covalent geometry : bond 0.00560 (17998) covalent geometry : angle 0.88815 (25112) hydrogen bonds : bond 0.06449 ( 733) hydrogen bonds : angle 5.75724 ( 2000) metal coordination : bond 0.00334 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 LEU cc_start: 0.9699 (mt) cc_final: 0.9421 (mt) REVERT: A 140 LEU cc_start: 0.9346 (tt) cc_final: 0.9089 (pp) REVERT: A 562 ASN cc_start: 0.8298 (t0) cc_final: 0.7581 (m-40) REVERT: A 566 MET cc_start: 0.8991 (tpt) cc_final: 0.8456 (tpt) REVERT: A 811 MET cc_start: 0.8833 (tmm) cc_final: 0.8171 (ppp) REVERT: A 818 LEU cc_start: 0.9443 (tp) cc_final: 0.9123 (mt) REVERT: A 912 LEU cc_start: 0.9324 (tp) cc_final: 0.9064 (tp) REVERT: A 955 MET cc_start: 0.9504 (mmm) cc_final: 0.9067 (mmp) REVERT: D 586 MET cc_start: 0.7100 (tpp) cc_final: 0.6257 (tpp) REVERT: D 601 MET cc_start: 0.8463 (mtt) cc_final: 0.8179 (mtt) REVERT: F 18 MET cc_start: 0.9609 (mmp) cc_final: 0.9294 (mmm) REVERT: F 59 TYR cc_start: 0.9186 (t80) cc_final: 0.8682 (t80) REVERT: F 61 ARG cc_start: 0.8647 (ttt-90) cc_final: 0.7789 (tmm160) REVERT: E 86 MET cc_start: 0.8432 (tpt) cc_final: 0.8065 (tpp) REVERT: E 117 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8150 (mt-10) REVERT: E 136 MET cc_start: 0.9172 (mmp) cc_final: 0.8971 (mmp) REVERT: E 162 ASP cc_start: 0.9310 (m-30) cc_final: 0.8975 (m-30) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1191 time to fit residues: 18.5367 Evaluate side-chains 72 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 106 optimal weight: 8.9990 chunk 93 optimal weight: 7.9990 chunk 152 optimal weight: 20.0000 chunk 155 optimal weight: 10.0000 chunk 99 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 75 optimal weight: 0.7980 chunk 177 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 ASN ** A 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 569 GLN ** A 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 702 GLN ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1014 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 656 GLN D 659 ASN ** F 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 GLN ** E 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 461 GLN ** 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 = 0.3360 r_free = 0.3360 target = 0.046186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.034341 restraints weight = 214358.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.035145 restraints weight = 144382.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.035788 restraints weight = 108474.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.036232 restraints weight = 88016.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.036478 restraints weight = 75348.769| |-----------------------------------------------------------------------------| r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.4564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 17999 Z= 0.190 Angle : 0.793 17.692 25112 Z= 0.411 Chirality : 0.049 0.990 2925 Planarity : 0.005 0.088 2584 Dihedral : 24.366 170.839 4350 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 22.12 Ramachandran Plot: Outliers : 0.07 % Allowed : 14.26 % Favored : 85.68 % Rotamer: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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 aren not related in a simple way. whole: -2.10 (0.21), residues: 1515 helix: 0.07 (0.19), residues: 658 sheet: -2.30 (0.40), residues: 157 loop : -2.68 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 131 TYR 0.031 0.002 TYR A1006 PHE 0.037 0.002 PHE A 634 TRP 0.021 0.002 TRP A 604 HIS 0.008 0.001 HIS A 234 Details of bonding type rmsd covalent geometry : bond 0.00385 (17998) covalent geometry : angle 0.79316 (25112) hydrogen bonds : bond 0.05495 ( 733) hydrogen bonds : angle 5.51847 ( 2000) metal coordination : bond 0.00142 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 LEU cc_start: 0.9685 (mt) cc_final: 0.9357 (mt) REVERT: A 140 LEU cc_start: 0.9293 (tt) cc_final: 0.9033 (pp) REVERT: A 562 ASN cc_start: 0.8261 (t0) cc_final: 0.7474 (m-40) REVERT: A 811 MET cc_start: 0.8741 (tmm) cc_final: 0.8262 (ppp) REVERT: A 955 MET cc_start: 0.9491 (mmm) cc_final: 0.8903 (mmm) REVERT: D 586 MET cc_start: 0.6707 (tpp) cc_final: 0.5849 (tpp) REVERT: F 18 MET cc_start: 0.9596 (mmp) cc_final: 0.9247 (mmm) REVERT: F 59 TYR cc_start: 0.9109 (t80) cc_final: 0.8829 (t80) REVERT: E 86 MET cc_start: 0.8309 (tpt) cc_final: 0.7699 (tmm) REVERT: E 146 TYR cc_start: 0.9261 (t80) cc_final: 0.8813 (t80) REVERT: E 162 ASP cc_start: 0.9251 (m-30) cc_final: 0.8863 (m-30) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.1141 time to fit residues: 17.8393 Evaluate side-chains 73 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 113 optimal weight: 8.9990 chunk 135 optimal weight: 0.7980 chunk 42 optimal weight: 10.0000 chunk 7 optimal weight: 8.9990 chunk 173 optimal weight: 7.9990 chunk 124 optimal weight: 0.5980 chunk 76 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 20 optimal weight: 20.0000 chunk 25 optimal weight: 7.9990 chunk 126 optimal weight: 5.9990 overall best weight: 4.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 569 GLN ** A 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 840 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 949 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1014 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 584 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 659 ASN ** F 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 GLN ** E 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.045158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.033408 restraints weight = 219343.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.034193 restraints weight = 147131.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.034875 restraints weight = 110424.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.035285 restraints weight = 89401.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 61)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.035662 restraints weight = 77202.490| |-----------------------------------------------------------------------------| r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.4682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 17999 Z= 0.249 Angle : 0.853 18.021 25112 Z= 0.444 Chirality : 0.050 0.948 2925 Planarity : 0.005 0.064 2584 Dihedral : 24.490 170.896 4350 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 27.70 Ramachandran Plot: Outliers : 0.07 % Allowed : 14.79 % Favored : 85.15 % Rotamer: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.47 % 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 aren not related in a simple way. whole: -2.28 (0.21), residues: 1515 helix: -0.15 (0.19), residues: 660 sheet: -2.34 (0.39), residues: 159 loop : -2.70 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 727 TYR 0.038 0.003 TYR D 565 PHE 0.025 0.002 PHE A 854 TRP 0.026 0.002 TRP A 604 HIS 0.008 0.001 HIS A 234 Details of bonding type rmsd covalent geometry : bond 0.00502 (17998) covalent geometry : angle 0.85336 (25112) hydrogen bonds : bond 0.06175 ( 733) hydrogen bonds : angle 5.71432 ( 2000) metal coordination : bond 0.00294 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 LEU cc_start: 0.9703 (mt) cc_final: 0.9429 (mt) REVERT: A 562 ASN cc_start: 0.8353 (t0) cc_final: 0.7748 (m-40) REVERT: A 811 MET cc_start: 0.8788 (tmm) cc_final: 0.8395 (ppp) REVERT: A 955 MET cc_start: 0.9513 (mmm) cc_final: 0.9044 (mmm) REVERT: D 586 MET cc_start: 0.6885 (tpp) cc_final: 0.5995 (tpp) REVERT: D 601 MET cc_start: 0.8300 (mtt) cc_final: 0.8053 (mtt) REVERT: F 18 MET cc_start: 0.9613 (mmp) cc_final: 0.9264 (mmm) REVERT: F 59 TYR cc_start: 0.9098 (t80) cc_final: 0.8607 (t80) REVERT: F 61 ARG cc_start: 0.8681 (ttt-90) cc_final: 0.7796 (tmm160) REVERT: E 86 MET cc_start: 0.8308 (tpt) cc_final: 0.7517 (tmm) REVERT: E 162 ASP cc_start: 0.9273 (m-30) cc_final: 0.8950 (m-30) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.1145 time to fit residues: 16.9560 Evaluate side-chains 68 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 64 optimal weight: 7.9990 chunk 40 optimal weight: 8.9990 chunk 154 optimal weight: 20.0000 chunk 9 optimal weight: 3.9990 chunk 179 optimal weight: 6.9990 chunk 81 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 166 optimal weight: 20.0000 chunk 138 optimal weight: 0.5980 chunk 115 optimal weight: 5.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 569 GLN A 636 ASN ** A 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 949 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1014 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1098 GLN ** D 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 659 ASN ** F 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 GLN E 127 HIS ** H 461 GLN ** 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 = 0.3347 r_free = 0.3347 target = 0.046130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.034304 restraints weight = 216139.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.035108 restraints weight = 146334.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.035811 restraints weight = 109669.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.036274 restraints weight = 88719.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.036562 restraints weight = 76055.599| |-----------------------------------------------------------------------------| r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.4993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 17999 Z= 0.179 Angle : 0.775 17.398 25112 Z= 0.402 Chirality : 0.048 0.985 2925 Planarity : 0.004 0.055 2584 Dihedral : 24.300 170.849 4350 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 22.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 14.32 % Favored : 85.61 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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 aren not related in a simple way. whole: -2.04 (0.21), residues: 1515 helix: 0.08 (0.19), residues: 660 sheet: -2.15 (0.42), residues: 148 loop : -2.65 (0.23), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 534 TYR 0.033 0.002 TYR D 565 PHE 0.028 0.002 PHE A 854 TRP 0.021 0.002 TRP A 604 HIS 0.025 0.002 HIS A 234 Details of bonding type rmsd covalent geometry : bond 0.00366 (17998) covalent geometry : angle 0.77456 (25112) hydrogen bonds : bond 0.05373 ( 733) hydrogen bonds : angle 5.50572 ( 2000) metal coordination : bond 0.00134 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 LEU cc_start: 0.9715 (mt) cc_final: 0.9386 (mt) REVERT: A 562 ASN cc_start: 0.8143 (t0) cc_final: 0.7296 (m-40) REVERT: A 740 ILE cc_start: 0.8534 (pt) cc_final: 0.8293 (tp) REVERT: A 811 MET cc_start: 0.8707 (tmm) cc_final: 0.8303 (ppp) REVERT: A 948 HIS cc_start: 0.8214 (m90) cc_final: 0.7922 (m90) REVERT: A 955 MET cc_start: 0.9535 (mmm) cc_final: 0.8933 (mmm) REVERT: D 586 MET cc_start: 0.6693 (tpp) cc_final: 0.6144 (tpp) REVERT: D 601 MET cc_start: 0.8260 (mtt) cc_final: 0.7985 (mtt) REVERT: F 18 MET cc_start: 0.9611 (mmp) cc_final: 0.9219 (mmm) REVERT: F 59 TYR cc_start: 0.9116 (t80) cc_final: 0.8607 (t80) REVERT: F 61 ARG cc_start: 0.8608 (ttt-90) cc_final: 0.7755 (tmm160) REVERT: E 86 MET cc_start: 0.8256 (tpt) cc_final: 0.7616 (tmm) REVERT: E 146 TYR cc_start: 0.9283 (t80) cc_final: 0.8675 (t80) REVERT: E 162 ASP cc_start: 0.9224 (m-30) cc_final: 0.8850 (m-30) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.1180 time to fit residues: 17.4982 Evaluate side-chains 72 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 13 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 171 optimal weight: 20.0000 chunk 35 optimal weight: 1.9990 chunk 178 optimal weight: 5.9990 chunk 145 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 chunk 23 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 569 GLN ** A 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 949 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 983 ASN ** A1014 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 584 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 GLN ** H 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.047081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.035197 restraints weight = 213119.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.036039 restraints weight = 142470.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.036733 restraints weight = 106968.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.037241 restraints weight = 86540.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.037552 restraints weight = 73829.563| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.5455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17999 Z= 0.151 Angle : 0.734 17.049 25112 Z= 0.381 Chirality : 0.047 0.992 2925 Planarity : 0.004 0.057 2584 Dihedral : 24.007 171.689 4350 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 19.92 Ramachandran Plot: Outliers : 0.07 % Allowed : 13.27 % Favored : 86.67 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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 aren not related in a simple way. whole: -1.77 (0.22), residues: 1515 helix: 0.32 (0.20), residues: 667 sheet: -1.91 (0.43), residues: 144 loop : -2.57 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 534 TYR 0.032 0.002 TYR D 565 PHE 0.035 0.002 PHE A 634 TRP 0.025 0.002 TRP A 604 HIS 0.012 0.001 HIS A 234 Details of bonding type rmsd covalent geometry : bond 0.00310 (17998) covalent geometry : angle 0.73410 (25112) hydrogen bonds : bond 0.04933 ( 733) hydrogen bonds : angle 5.29593 ( 2000) metal coordination : bond 0.00060 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 LEU cc_start: 0.9720 (mt) cc_final: 0.9386 (mt) REVERT: A 140 LEU cc_start: 0.9252 (tt) cc_final: 0.8978 (pp) REVERT: A 546 MET cc_start: 0.7337 (mmm) cc_final: 0.7018 (mmm) REVERT: A 562 ASN cc_start: 0.8327 (t0) cc_final: 0.7898 (t0) REVERT: A 569 GLN cc_start: 0.9579 (tt0) cc_final: 0.8884 (tp-100) REVERT: A 740 ILE cc_start: 0.8452 (pt) cc_final: 0.8138 (tp) REVERT: A 811 MET cc_start: 0.8533 (tmm) cc_final: 0.8203 (ppp) REVERT: A 955 MET cc_start: 0.9451 (mmm) cc_final: 0.9009 (mmm) REVERT: D 586 MET cc_start: 0.6617 (tpp) cc_final: 0.6062 (tpp) REVERT: F 59 TYR cc_start: 0.9062 (t80) cc_final: 0.8645 (t80) REVERT: F 61 ARG cc_start: 0.8583 (ttt-90) cc_final: 0.7930 (tmm160) REVERT: E 86 MET cc_start: 0.8212 (tpt) cc_final: 0.7487 (tmm) REVERT: E 117 GLU cc_start: 0.8356 (mm-30) cc_final: 0.8037 (mt-10) REVERT: E 146 TYR cc_start: 0.9248 (t80) cc_final: 0.8802 (t80) REVERT: E 162 ASP cc_start: 0.9051 (m-30) cc_final: 0.8746 (m-30) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.1215 time to fit residues: 19.4042 Evaluate side-chains 78 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 161 optimal weight: 20.0000 chunk 72 optimal weight: 5.9990 chunk 44 optimal weight: 0.0870 chunk 53 optimal weight: 0.9980 chunk 171 optimal weight: 20.0000 chunk 85 optimal weight: 5.9990 chunk 42 optimal weight: 8.9990 chunk 58 optimal weight: 0.4980 chunk 68 optimal weight: 3.9990 chunk 126 optimal weight: 6.9990 chunk 160 optimal weight: 40.0000 overall best weight: 2.3162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 833 GLN ** A 945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1014 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 584 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 GLN ** H 461 GLN ** 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 = 0.3368 r_free = 0.3368 target = 0.046789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.034851 restraints weight = 215376.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.035719 restraints weight = 144369.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.036411 restraints weight = 108241.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 71)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.036888 restraints weight = 87643.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 63)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.037226 restraints weight = 75122.784| |-----------------------------------------------------------------------------| r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.5586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17999 Z= 0.162 Angle : 0.738 17.065 25112 Z= 0.383 Chirality : 0.047 0.975 2925 Planarity : 0.004 0.053 2584 Dihedral : 23.972 171.655 4350 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 21.47 Ramachandran Plot: Outliers : 0.07 % Allowed : 13.53 % Favored : 86.40 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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 aren not related in a simple way. whole: -1.73 (0.22), residues: 1515 helix: 0.37 (0.20), residues: 661 sheet: -1.96 (0.42), residues: 150 loop : -2.52 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 534 TYR 0.035 0.002 TYR D 565 PHE 0.028 0.002 PHE A 854 TRP 0.024 0.002 TRP A 604 HIS 0.012 0.001 HIS A 234 Details of bonding type rmsd covalent geometry : bond 0.00331 (17998) covalent geometry : angle 0.73761 (25112) hydrogen bonds : bond 0.05060 ( 733) hydrogen bonds : angle 5.24495 ( 2000) metal coordination : bond 0.00136 ( 1) =============================================================================== Job complete usr+sys time: 3254.33 seconds wall clock time: 57 minutes 11.84 seconds (3431.84 seconds total)